Temporal range: 250–0Ma Triassic - Present
The dinoflagellates (Greek δῖνος dinos "whirling" and Latin flagellum "whip, scourge") are a large group of flagellate protists. Most are marine plankton, but they are common in fresh water habitats as well. Their populations are distributed depending on temperature, salinity, or depth. Many dinoflagellates are known to be photosynthetic, but a large fraction of these are in fact mixotrophic, combining photosynthesis with ingestion of prey. In terms of number of species, dinoflagellates form one of the largest groups of marine eukaryotes, although this group is substantially smaller than the diatoms. Some species are endosymbionts of marine animals and play an important part in the biology of coral reefs. Other dinoflagellates are colorless predators on other protozoa, and a few forms are parasitic (see for example Oodinium, Pfiesteria). Some dinoflagellates produce resting stages, called dinoflagellate cysts or dinocysts, as part of their life cycles.
About 1,555 species of free-living marine dinoflagellates are currently described. Another estimate suggests ca. 2,000 living species, of which more than 1,700 are marine and about 220 are from freshwater. The latest estimates suggest a total of 2,294 living dinoflagellate species, which includes marine, freshwater and parasitic dinoflagellates.
In 1753, the first modern dinoflagellates were described by Henry Baker as "Animalcules which cause the Sparkling Light in Sea Water", and named by Otto Friedrich Müller in 1773. The term derives from the Greek word δῖνος (dinos), meaning 'whirling,' and Latin flagellum, a diminutive term for a whip or scourge.
In the 1830s, the German microscopist Christian Gottfried Ehrenberg examined many water and plankton samples and proposed several dinoflagellate genera that are still used today including Peridinium, Prorocentrum and Dinophysis.
These same dinoflagellates were first defined by Otto Bütschli in 1885 as the flagellate order Dinoflagellida. Botanists treated them as a division of algae, named Pyrrophyta or Pyrrhophyta ("fire algae"; Greek pyrr(h)os, fire) after the bioluminescent forms, or Dinophyta. At various times, the cryptomonads, ebriids, and ellobiopsids have been included here, but only the last are now considered close relatives. Dinoflagellates have a known ability to transform from noncyst to cyst-forming strategies, which makes recreating their evolutionary history extremely difficult.
Dinoflagellates are protists which have been classified using both the International Code of Botanical Nomenclature (ICBN, now renamed as ICN) and the International Code of Zoological Nomenclature (ICZN). Approximately half of living dinoflagellate species are autotrophs possessing chloroplasts and half are non-photosynthesising heterotrophs. It is now widely accepted that the ICN should be used for their classification.
Most (but not all) dinoflagellates have a dinokaryon, described below (see: Life-cycle, below). Dinoflagellates with a dinokaryon are classified under Dinokaryota, while dinoflagellates without a dinokaryon are classified under Syndiniales.
Although classified as eukaryotes, the dinoflagellate nuclei are not characteristically eukaryotic, as they lack histones, nucleosomes and maintain continually condensed chromosomes during mitosis. In fact, Dodge (1966) termed the dinoflagellate nucleus as ‘mesokaryotic’, due to its possession of intermediate characteristics between the coiled DNA areas of prokaryotic bacteria and the well-defined eukaryotic nucleus. This group, however, does contain typically eukaryotic organelles, such as Golgi bodies, mitochondria and chloroplasts.
Jakob Schiller (1931–1937) provided a description of all the species, both marine and freshwater, known at that time. Later Alain Sournia (1973, 1978, 1982, 1990, 1993) listed the new taxonomic entries published after Schiller (1931–1937). Sournia (1986) gave descriptions and illustrations of the marine genera of dinoflagellates, excluding information at the species level. The latest index is written by Gomez.
English-language taxonomic monographs covering large numbers of species are published for the Gulf of Mexico, the Indian Ocean, the British Isles, the Mediterranean and the North Sea.
The main source for identification of freshwater dinoflagellates is the Süsswasser Flora.
Dinoflagellates are unicellular and possess two dissimilar flagellae arising from the ventral cell side (dinokont flagellation). They have a ribbon-like transverse flagellum with multiple waves that beats to the cell’s left, and a more conventional one, the longitudinal flagellum, that beats posteriorly,. The transverse flagellum is a wavy ribbon in which only the outer edge undulates from base to tip, due to the action of the axoneme which runs along it. The axonemal edge has simple hairs that can be of varying length. The flagellar movement produces forward propulsion and also a turning force. The longitudinal flagellum is relatively conventional in appearance, with few or no hairs. It beats with only one or two periods to its wave. The flagella lie in surface grooves: the transverse one in the cingulum and the longitudinal one in the sulcus, although its distal portion projects freely behind the cell. In dinoflagellate species with desmokont flagellation (e.g., Prorocentrum) the two flagella are differentiated as in dinokonts, but they are not associated with grooves.
Dinoflagellates have a complex cell covering called an amphiesma or cortex, composed of a series of membrances, flattened vesicles called alveolae (=amphiesmal vesicles) and related structures. In armoured dinoflagellates, these support overlapping cellulose plates to create a sort of armor called the theca, as opposed to athecate dinoflagellates. These come in various shapes and arrangements, depending on the species and sometimes on the stage of the dinoflagellate. Conventionally, the term tabulation has been used to refer to this arrangement of thecal plates. The plate configuration can be denoted with the plate formula or tabulation formula. Fibrous extrusomes are also found in many forms. Together with various other structural and genetic details, this organization indicates a close relationship between the dinoflagellates, Apicomplexa, and ciliates, collectively referred to as the alveolates.
The chloroplasts in most photosynthetic dinoflagellates are bound by three membranes, suggesting they were probably derived from some ingested algae. Most photosynthetic species contain chlorophylls a and c2, the carotenoid beta-carotene, and a group of xanthophylls that appears to be unique to dinoflagellates, typically peridinin, dinoxanthin, and diadinoxanthin. These pigments give many dinoflagellates their typical goldenbrown color. However, the dinoflagellates Karenia brevis, Karenia mikimotoi and Karlodinium micrum have acquired other pigments through endosymbiosis, including fucoxanthin. This suggests their chloroplasts were incorporated by several endosymbiotic events involving already colored or secondarily colorless forms. The discovery of plastids in Apicomplexa has led some to suggest they were inherited from an ancestor common to the two groups, but none of the more basal lines have them. All the same, the dinoflagellate cell consists of the more common organelles such as rough and smooth endoplasmic reticulum, Golgi apparatus, mitochondria, lipid and starch grains, and food vacuoles. Some have even been found with a light-sensitive organelle, the eyespot or stigma, or a larger nucleus containing a prominent nucleolus. The dinoflagellate Erythropsidium has the smallest known eye.
Some athecate species have an internal skeleton consisting of two star-like siliceous elements that has an unknown function, and can be found as microfossils. Tappan gave a survey of dinoflagellates with internal skeletons. This included the first detailed description of the pentasters in Actiniscus pentasterias, based on scanning electron microscopy. They are placed within the order Gymnodiniales, suborder Actiniscineae.
Most zooxanthellae are dinoflagellates. The association between dinoflagellates and reef-building corals is widely known, but dinoflagellate endosymbionts inhabit a great number of other invertebrates and protists, for example many sea anemones, jellyfish, nudibranchs, the giant clam Tridacna, as well as several species of radiolarians and foraminiferans. Many extant dinoflagellates are parasites (here defined as organisms that eat their prey from the inside, i.e. endoparasites, or that remain attached to their prey for longer periods of time, i.e. ectoparasites). They can parasitize animal or protist hosts. Protoodinium, Crepidoodinium, Piscinoodinium and Blastodinium retain their plastids while feeding on their zooplanktonic or fish hosts. In most parasitic dinoflagellates the infective stage resembles a typical motile dinoflagellate cell.
Theca structure and formation 
The formation of thecal plates has been studied in detail through ultrastructural studies.
Dinoflagellates can occur in all aquatic environments: marine, brackish, and fresh water, including in snow or ice. They are also common in benthic environments and in sea ice.
Nutritional strategies 
There are several nutritional strategies in dinoflagellates: phototrophy, mixotrophy and heterotrophy. Phototrophs can be photoautotrophs or auxotrophs. Mixotrophic dinoflagellates are photosynthetically active, but are also heterotrophic. Facultative mixotrophs, in which autotrophy or heterotrophy is sufficient for nutrition, are classified as amphitrophic. If both forms are required the organisms are mixotrophic sensu stricto. Some free-living dinoflagellates do not have chloroplasts but host a phototrophic endosymbiont. A few dinoflagellates may utilize alien chloroplasts (cleptochloroplasts), obtained from food (kleptoplasty). Some dinoflagellates may feed on other organisms as predators or parasites.
Mechanisms of capture and ingestion in dinoflagellates are quite diverse. Several dinoflagellates, both thecate (e.g. Ceratium hirundinella,; Peridinium globulus,) and nonthecate (e.g. Oxyrrhis marina, Gymnodinium sp. and Kofoidinium spp.), draw prey to the sulcal region of the cell (either via water currents set up by the flagella or via pseudopodial extensions) and ingest the prey through the sulcus. In several Protoperidinium spp., e.g. Protoperidinium conicum, a large feeding veil - a pseudopod called the pallium - is extruded to capture prey which is subsequently digested extracellularly (=pallium-feeding). Oblea, Zygabikodinium and Diplopsalis are the only other dinoflagellate genera known to use this particular feeding mechanism ). Katodinium (Gymnodinium) fungiforme, commonly found as a contaminant in algal or ciliate cultures, feeds by attaching to its prey and ingesting prey cytoplasm through an extensible peduncle. The feeding mechanisms of the oceanic dinoflagellates remain unknown, although pseudopodial extensions were observed in Podolampas bipes.
The dinoflagellate nucleus: Dinokaryon 
Most dinoflagellates have a peculiar form of nucleus, called a dinokaryon, in which the chromosomes are attached to the nuclear membrane. These lack histones and remain condensed throughout interphase rather than just during mitosis, which is closed and involves a unique external spindle. This sort of nucleus was once considered to be an intermediate between the nucleoid region of prokaryotes and the true nuclei of eukaryotes, so were termed mesokaryotic, but now are considered advanced rather than primitive traits.
Life cycle 
Dinoflagellates have a haplontic life cycle - with the possible exception of Noctiluca and its relatives. The life-cycle usually involves asexual reproduction by means of binary fission, either through desmoschisis or eleuteroschisis. More complex life cycles occur, more particularly with parasitic dinofagellates. Sexual reproduction also occurs (e.g.) and is only known in a small percentage of dinoflagellates. This takes place by fusion of two individuals to form a zygote, which may remain mobile in typical dinoflagellate fashion and is then called a planozygote. This zygote may later form a resting stage or hypnozygote, which are called dinoflagellate cyst or dinocyst. After (or before) germination of the cyst, the hatchling undergoes meiosis to produce new haploid cells.
Harmful algal blooms 
Dinoflagellates sometimes bloom in concentrations of more than a million cells per millilitre. Some species produce neurotoxins, which in such quantities kill fish and accumulate in filter feeders such as shellfish, which in turn may pass them on to people who eat them. This phenomenon is called a red tide, from the color the bloom imparts to the water. Some colorless dinoflagellates may also form toxic blooms, such as Pfiesteria. Some dinoflagellate blooms are not dangerous. Bluish flickers visible in ocean water at night often come from blooms of bioluminescent dinoflagellates, which emit short flashes of light when disturbed.
The same red tide mentioned above is more specifically produced when dinoflagellates are able to reproduce rapidly and copiously on account of the abundant nutrients in the water. Although the resulting red waves are an unusual sight, they contain toxins that not only affect all marine life in the ocean, but the people who consume them, as well. A specific carrier is shellfish. This can introduce both nonfatal and fatal illnesses. One such poison is saxitoxin, a powerful paralytic. Human inputs of phosphate further encourage these red tides, so there is a strong interest in learning more about dinoflagellates, from both medical and economic perspectives. The ecology of harmful algal blooms is extensively studied.
Lipid and sterol production 
These species contain scintillons, individual cytoplasmic bodies (ca. 0.5 µm in diameter) distributed mainly in the cortical region of the cell, outpockets of the main cell vacuole. They contain dinoflagellate luciferase, the main enzyme involved in dinoflagellate bioluminescence, and luciferin, a chlorophyll-derived tetrapyrrole ring that acts as the substrate to the light-producing reaction. The luminescence occurs as a brief (0.1 sec) blue flash (max 476 nm) when stimulated, usually by mechanical disturbance. Therefore, when mechanically stimulated—by boat, swimming or waves, for example—a blue sparkling light can be seen emanating from the sea surface.
Dinoflagellate bioluminescence is controlled by circadian rhythms and only occurs at night (e.g.,). Luminescent and nonluminescent strains can occur in the same species.
The luciferin-luciferase reaction responsible for the bioluminescence is pH sensitive. When the pH drops, luciferase changes its shape, allowing luciferin, more specifically tetrapyrrole, to bind. Dinoflagellates can use bioluminescence as a defense mechanism. They can startle their predators by their flashing light or they can ward off potential predators by an indirect effect such as the burglar alarm. The dinoflagellate can use its bioluminescence to attract attention to itself, thereby bringing attention to the predator and making the predator more vulnerable to predators from higher trophic levels.
Bioluminescent dinoflagellate ecosystem bays are among the rarest and most fragile, with the most famous one Mosquito Bay in Vieques, Puerto Rico. There is a bioluminescent lagoon near Montego Bay, Jamaica.
One of the most striking features is the large amount of cellular DNA that dinoflagellates contain. Most eukaryotic algae contain on average about 0.54 pg DNA/cell, whereas estimates of dinoflagellate DNA content range from 3–250 pg/cell, corresponding to approximately 3000–215 000 Mb (in comparison, the haploid human genome is 3180 Mb and hexaploid Triticum wheat is 16 000 Mb). It has been suggested that polyploidy or polyteny may account for this large cellular DNA content, but studies of DNA reassociation kinetics do not support this hypothesis.
In addition to their disproportionately large genomes, dinoflagellate nuclei are unique in their morphology, regulation, and composition.
The dinoflagellates share an unusual mitochondrial genome organisation with their relatives, the Apicomplexa. Both groups have very reduced mitochondrial genomes (~6 kilobases in the Apicomplexa). The genes on the dinoflagellate genomes have undergone a number of reorganisations, including massive genome amplification and recombination which have resulted in multiple copies of each gene and gene fragments linked in numerous combinations. Loss of the standard stop codons, trans-splicing of mRNAs for the mRNA of cox3 and extensive RNA editing recoding of most genes has occurred. The reasons for this transformation are unknown.
Evolutionary history 
Dinoflagellates are mainly represented as fossils by fossil dinocysts, which have a long geological record with lowest occurrences during the mid-Triassic., whilst geochemical markers suggest a presence to the Early Cambrian.
Molecular phylogenetics shows that dinoflagellates are grouped with ciliates and apicomplexans (=Sporozoa) in a well-supported clade, the alveolates. The closest relatives to dinokaryotic dinoflagellates appear to be apicomplexans, Perkinsus, Parvilucifera, syndinians and Oxyrrhis. Molecular phylogenies are similar to phylogenies based on morphology.
Dinoflagellate evolution has been summarized into five principal organizational types: prorocentroid, dinophysoid, gonyaulacoid, peridinioid and gymnodinoid. The transitions of marine species into freshwater have been infrequent events during the diversification of dinoflagellates and in most cases have not occurred recently, possibly as late as the Cretaceous.
- Lingulodinium polyedrum
- Noctiluca (sea ghost or "fire of sea")
- Symbiodinium (Zooxanthella, a coral endosymbiont)
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