Synechococcus is a unicellular cyanobacterium that is very widespread in the marine environment
An ocean is a major body of saline water, and a principal component of the hydrosphere. Approximately 71% of the Earth's surface is covered by ocean, a continuous body of water that is customarily divided into several principal oceans and smaller seas.More than half of this area is over 3,000...

. Its size varies from 0.8 µm
A micrometer , is by definition 1×10-6 of a meter .In plain English, it means one-millionth of a meter . Its unit symbol in the International System of Units is μm...

 to 1.5 µm. The photosynthetic coccoid cells
Coccus can be used to describe any bacterium that has a spherical shape. It is one of the three distinct types of bacteria shapes, the other two being bacillus and spirillum cells...

 are preferentially found in well–lit surface water
Surface water
Surface water is water collecting on the ground or in a stream, river, lake, wetland, or ocean; it is related to water collecting as groundwater or atmospheric water....

s where it can be very abundant (generally 1,000 to 200,000 cells per millilitre). Many freshwater
Fresh Water
Fresh Water is the debut album by Australian rock and blues singer Alison McCallum, released in 1972. Rare for an Australian artist at the time, it came in a gatefold sleeve...

 species of Synechococcus have also been described.

The genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....

 of Synechococcus elongatus strain PCC7002 has a size of 2.7 Mbp
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...

, that of the oceanic strain WH8102 is 2.4 Mbp.


Synechococcus is one of the most important components of the prokaryotic
The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...

An autotroph, or producer, is an organism that produces complex organic compounds from simple inorganic molecules using energy from light or inorganic chemical reactions . They are the producers in a food chain, such as plants on land or algae in water...

ic picoplankton
Picoplankton is the fraction of plankton composed by cells between 0.2 and 2 μm that can be either :* photosynthetic * heterotrophic Some species can also be mixotrophic....

 in the temperate
In geography, temperate or tepid latitudes of the globe lie between the tropics and the polar circles. The changes in these regions between summer and winter are generally relatively moderate, rather than extreme hot or cold...

 to tropical
The tropics is a region of the Earth surrounding the Equator. It is limited in latitude by the Tropic of Cancer in the northern hemisphere at approximately  N and the Tropic of Capricorn in the southern hemisphere at  S; these latitudes correspond to the axial tilt of the Earth...

 oceans. The genus was first described in 1979, and was originally defined to include "small unicellular cyanobacteria with ovoid to cylindrical cells that reproduce by binary traverse fission in a single plane and lack sheaths". This definition of the genus Synechococcus contained organisms of considerable genetic diversity and was later subdivided into subgroups based on the presence of the accessory pigment phycoerythrin
Phycoerythrin is a red protein from the light-harvesting phycobiliprotein family, present in cyanobacteria, red algae and cryptomonads.Like all phycobiliproteins, phycoerythrin is composed of a protein part, organised in a hexameric structure of alpha and beta chains, covalently binding...

. The marine forms of Synechococcus are coccoid cells between 0.6 µm and 1.6 µm in size. They are gram negative cells with highly structured cell walls that may contain projections on their surface. Electron microscopy frequently reveals the presence of phosphate inclusions, glycogen
Glycogen is a molecule that serves as the secondary long-term energy storage in animal and fungal cells, with the primary energy stores being held in adipose tissue...

 granules and more importantly highly structured carboxysome
Carboxysomes are bacterial microcompartments that contain enzymes involved in carbon fixation. Carboxysomes are made of polyhedral protein shells about 80 to 140 nanometres in diameter. These compartments are thought to concentrate carbon dioxide to overcome the inefficiency of RuBisCo - the...


Cells are known to be motile by a gliding type method and a novel uncharacterized, non-phototactic swimming method that does not involve flagellar motion. While some cyanobacteria are capable of photoheterotrophic or even chemoheterotrophic growth, all marine Synechococcus strains appear to be obligate photoautotrophs that are capable of supporting their nitrogen requirements using nitrate, ammonia or in some cases urea
Urea or carbamide is an organic compound with the chemical formula CO2. The molecule has two —NH2 groups joined by a carbonyl functional group....

 as a sole nitrogen
Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...

 source. Marine Synechococcus are traditionally not thought to fix nitrogen (This perception may be changing).


The main photosynthetic pigment in Synechococcus in chlorophyll a
Chlorophyll a
Chlorophyll a is a specific form of chlorophyll used in oxygenic photosynthesis. It absorbs most energy from wavelengths of violet-blue and orange-red light. This photosynthetic pigment is essential for photosynthesis in eukaryotes, cyanobacteria and prochlorophytes because of its role as primary...

, while its major accessory pigments are phycobilliproteins. The four commonly recognized phycobilin
Phycobilins are chromophores found in cyanobacteria and in the chloroplasts of red algae, glaucophytes and some cryptomonads...

s are phycocyanin
Phycocyanin is a pigment from the light-harvesting phycobiliprotein family, along with allophycocyanin and phycoerythrin. It is an accessory pigment to chlorophyll. All phycobiliproteins are water-soluble and therefore cannot exist within the membrane as do carotenoids, but aggregate forming...

, allophycocyanin
Allophycocyanin is a protein from the light-harvesting phycobiliprotein family, along with phycocyanin, phycoerythrin and phycoerythrocyanin. It is an accessory pigment to chlorophyll...

, allophycocyanin B and phytoerythrin. In addition Synechococcus also contains zeaxanthin
Zeaxanthin is one of the most common carotenoid alcohols found in nature. It is important in the xanthophyll cycle. Synthesized in plants & some micro-organisms, it is the pigment that gives paprika , corn, saffron, and many other plants & microbes their characteristic color.The name is derived...

 but no diagnostic pigment for this organism is known. Zeaxanthin is also found in Prochlorococcus
Prochlorococcus is a genus of very small marine cyanobacteria with an unusual pigmentation . These bacteria belong to the photosynthetic picoplankton and are probably the most abundant photosynthetic organism on Earth....

, red algae
Red algae
The red algae are one of the oldest groups of eukaryotic algae, and also one of the largest, with about 5,000–6,000 species  of mostly multicellular, marine algae, including many notable seaweeds...

 and as a minor pigment in some chlorophytes
Chlorophyta is a division of green algae, informally called chlorophytes. The name is used in two very different senses so that care is needed to determine the use by a particular author...

 and eustigmatophyte
Eustigmatophytes are a small group of eukaryotic algae that includes marine, freshwater and soil-living species. All eustigmatophytes are unicellular, with coccoid cells and polysaccharide cell walls. Eustigmatophytes contain one or more yellow-green chloroplasts, which contain chlorophyll a and...

s. Similarly phycoerythrin is also found in rhodophytes and some cryptomonad
The cryptomonads are a group of algae, most of which have plastids. They are common in freshwater, and also occur in marine and brackish habitats. Each cell is around 10-50 μm in size and flattened in shape, with an anterior groove or pocket...



In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...

 description of Synechococcus is difficult. Isolates are morphologically
Morphology (biology)
In biology, morphology is a branch of bioscience dealing with the study of the form and structure of organisms and their specific structural features....

 very similar, yet exhibit a G+C content
In molecular biology and genetics, GC-content is the percentage of nitrogenous bases on a DNA molecule that are either guanine or cytosine . This may refer to a specific fragment of DNA or RNA, or that of the whole genome...

 ranging from 39% to 71%, illustrating the large genetic diversity of this provisional taxon. Initially attempts were made to divide the group into three sub-clusters, each with a specific range of genomic G+C content. The observation that open-ocean isolates alone nearly span the complete G+C spectrum however indicates that Synechococcus is composed of at least several species. Bergey's Manual (Herdman et al. 2001) now divides Synechococcus into five clusters (equivalent to genera) based on morphology, physiology and genetic traits.

Cluster one includes relatively large (1–1.5 µm) non-motile obligate photoautotrophs that exhibit low salt tolerance. Reference strains for this cluster are PCC6301 (formerly Anacycstis nidulans) and PCC6312, which were isolated from freshwater in Texas
Texas is the second largest U.S. state by both area and population, and the largest state by area in the contiguous United States.The name, based on the Caddo word "Tejas" meaning "friends" or "allies", was applied by the Spanish to the Caddo themselves and to the region of their settlement in...

 and California
California is a state located on the West Coast of the United States. It is by far the most populous U.S. state, and the third-largest by land area...

 respectively. Cluster 2 also is characterized by low salt tolerance. Cells are obligate photoautrotrophs, lack phycoerythrin and are thermophilic. The reference strain PCC6715 was isolated from a hot spring in Yellowstone National Park
Yellowstone National Park
Yellowstone National Park, established by the U.S. Congress and signed into law by President Ulysses S. Grant on March 1, 1872, is a national park located primarily in the U.S. state of Wyoming, although it also extends into Montana and Idaho...

. Cluster 3 includes phycoerythrin lacking marine Synechococcus that are euryhaline i.e. capable of growth in both marine and fresh water environments. Several strains, including the reference strain PCC7003 are facultative heterotrophs and require vitamin B12 for growth. Cluster 4 contains a single isolate, PCC7335. This strain is obligate marine. This strain contains phycoerthrin and was first isolated from the intertidal zone in Puerto Peñasco
Puerto Peñasco
Puerto Peñasco is a city and municipality located in the northwest of the state of Sonora about 100 km from the Arizona border. It is located on the small strip of land that joins the peninsula of Baja California with the rest of Mexico. The area is part of the Altar Desert, one of the driest...

, Mexico
The United Mexican States , commonly known as Mexico , is a federal constitutional republic in North America. It is bordered on the north by the United States; on the south and west by the Pacific Ocean; on the southeast by Guatemala, Belize, and the Caribbean Sea; and on the east by the Gulf of...

. The last cluster contains what had previously been referred to as ‘marine A and B clusters’ of Synechococcus. These cells are truly marine and have been isolated from both the coastal and the open ocean. All strains are obligate photoautrophs and are around 0.6–1.7 µm in diameter. This cluster is however further divided into a population that either contains (cluster 5.1) or does not contain (cluster 5.2) phycoerythrin. The reference strains are WH8103 for the phycoerythrin containing strains and WH5701 for those strains that lack this pigment (Waterbury et al. 1986b). More recently Badger et al. (2002) proposed the division of the cyanobacteria into a α- and a β-subcluster based on the type of rbcL (large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase) found in these organisms. α-cyanobacteria were defined to contain a form IA, while β-cyanobacteria were defined to contain a form IB of this gene. In support for this division Badger et al. analyze the phylogeny of carboxysomal proteins, which appear to support this division. Also, two particular bicarbonate transport systems appear to only be found in α-cyanobacteria, which lack carboxysomal carbonic anhydrases.

Ecology and distribution

Synechococcus has been observed to occur at concentrations ranging between a few cells per ml to 106 cells per ml in virtually all regions of the oceanic euphotic zone except in samples from the McMurdo Sound
McMurdo Sound
The ice-clogged waters of Antarctica's McMurdo Sound extend about 55 km long and wide. The sound opens into the Ross Sea to the north. The Royal Society Range rises from sea level to 13,205 feet on the western shoreline. The nearby McMurdo Ice Shelf scribes McMurdo Sound's southern boundary...

 and Ross Ice Shelf
Ross Ice Shelf
The Ross Ice Shelf is the largest ice shelf of Antarctica . It is several hundred metres thick. The nearly vertical ice front to the open sea is more than 600 km long, and between 15 and 50 metres high above the water surface...

 in Antarctica. Cells are generally much more abundant in nutrient rich environments than in the oligotrophic ocean and prefer the upper well-lit portion of the euphotic zone. Synechococcus has also been observed to occur at high abundances in environments with low salinities and/or low temperatures. Synechococcus is usually far outnumbered by Prochlorococcus in all environments, where they co-occur. Exceptions to this rule are areas of permanently enriched nutrients such as upwelling
Upwelling is an oceanographic phenomenon that involves wind-driven motion of dense, cooler, and usually nutrient-rich water towards the ocean surface, replacing the warmer, usually nutrient-depleted surface water. The increased availability in upwelling regions results in high levels of primary...

 areas and coastal watersheds. In the nutrient deplete areas of the oceans, such as the central gyres, Synechococcus is apparently always present, although only at low concentrations ranging from a few to 4×10³ cells per ml. Vertically Synechococcus is usually relatively equitably distributed throughout the mixed layer and exhibits an affinity for the higher light regime. Below the mixed layer, cell concentrations rapidly decline. Vertical profiles are however strongly influenced by hydrologic conditions and can be very variable both seasonally and spatially. Overall Synechococcus abundance often parallels that of Prochlorococcus in the water column. In the Pacific HNLC (High Nutrient Low Chlorophyll) zone and in temperate open seas where stratification was recently established both profiles parallel each other and exhibit abundance maxima just about the SCM.

The factors controlling the abundance of Synechococcus still remain poorly understood, especially considering that even in the most nutrient deplete regions of the central gyres, where cell abundances are often very low, population growth rates are often high and not very drastically limited. Factors such as grazing, viral mortality, genetic variability, light adaptation, temperature as well as nutrients are certainly involved, but remain to be investigated on a rigorous and global scale. Despite the uncertainties it has been suggested that there is at least a relationship between ambient nitrogen concentrations and Synechococcus abundance and an inverse relationship to Prochlorococcus in the upper euphotic zone, where light is not limiting. One environment where Synechococcus thrives particularly well are coastal plumes of major rivers. Such plumes are coastally enriched with nutriets such as nitrate and phosphate, which drives large phytoplankton blooms. High productivity in coastal river plumes is often associated with large populations of Synechococcus and elevated form IA (cyanobacterial) rbcL mRNA.

It should also be noted that Prochlorococcus is thought to be at least 100 times more abundant than Synechococcus in warm oligotrophic waters. Assuming average cellular carbon concentrations it has thus been estimated that Prochlorococcus accounts for at least 22 times more carbon in these waters and may thus be of much greater significance to the global carbon cycle than Synechococcus.


  • S. ambiguus Skuja
  • S. arcuatus var. calcicolus Fjerdingstad
  • S. bigranulatus Skuja
  • S. brunneolus Rabenhorst
  • S. caldarius Okada
  • S. capitatus A. E. Bailey-Watts & J. Komárek
  • S. carcerarius Norris
  • S. elongatus (Nägeli) Nägeli
  • S. endogloeicus F. Hindák
  • S. epigloeicus F. Hindák
  • S. ferrunginosus Wawrik
  • S. intermedius Gardner
  • S. koidzumii Yoneda
  • S. lividus Copeland
  • S. marinus Jao
  • S. minutissimus Negoro
  • S. mundulus Skuja

  • S. nidulans (Pringsheim) Komárek
  • S. rayssae Dor
  • S. rhodobaktron Komárek & Anagnostidis
  • S. roseo-persicinus Grunow
  • S. roseo-purpureus G. S. West
  • S. salinarum Komárek
  • S. salinus Frémy
  • S. sciophilus Skuja
  • S. sigmoideus (Moore & Carter) Komárek
  • S. spongiarum Usher et al.
  • S. subsalsus Skuja
  • S. sulphuricus Dor
  • S. vantieghemii (Pringsheim) Bourrelly
  • S. violaceus Grunow
  • S. viridissimus Copeland
  • S. vulcanus Copeland
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