Ciliate

The ciliates are a group of alveolates characterized by the presence of hair-like organelles called cilia, which are identical in structure to eukaryotic flagella, but are in general shorter and present in much larger numbers, with a different undulating pattern than flagella. Cilia occur in all members of the group (although the peculiar Suctoria only have them for part of their life cycle) and are variously used in swimming, crawling, attachment, feeding, and sensation.

Ciliates are an important group of protists, common almost anywhere there is water—in lakes, ponds, oceans, rivers, and soils, including anoxic and oxygen-depleted habitats. About 4,500 unique free-living species have been described, and the potential number of extant species is estimated at 27,000–40,000. Included in this number are many ectosymbiotic and endosymbiotic species, as well as some obligate and opportunistic parasites. Ciliate species range in size from as little as 10 μm in some colpodeans to as much as 4 mm in length in some geleiids, and include some of the most morphologically complex protozoans.

In most systems of taxonomy, "Ciliophora" is ranked as a phylum under any of several kingdoms, including Chromista, Protista or Protozoa. In some older systems of classification, such as the influential taxonomic works of Alfred Kahl, ciliated protozoa are placed within the class "Ciliata" (a term which can also refer to a genus of fish). In the taxonomic scheme endorsed by the International Society of Protistologists, which eliminates formal rank designations such as "phylum" and "class", "Ciliophora" is an unranked taxon within Alveolata.

Unlike most other eukaryotes, ciliates have two different sorts of nuclei: a tiny, diploid micronucleus (the "generative nucleus", which carries the germline of the cell), and a large, ampliploid macronucleus (the "vegetative nucleus", which takes care of general cell regulation, expressing the phenotype of the organism). The latter is generated from the micronucleus by amplification of the genome and heavy editing. The micronucleus passes its genetic material to offspring, but does not express its genes. The macronucleus provides the small nuclear RNA for vegetative growth.

Division of the macronucleus occurs in most ciliate species, apart from those in class Karyorelictea, whose macronuclei are replaced every time the cell divides. Macronuclear division is accomplished by amitosis, and the segregation of the chromosomes occurs by a process whose mechanism is unknown. After a certain number of generations (200–350, in Paramecium aurelia, and as many as 1,500 in Tetrahymena) the cell shows signs of aging, and the macronuclei must be regenerated from the micronuclei. Usually, this occurs following conjugation, after which a new macronucleus is generated from the post-conjugal micronucleus.

Food vacuoles are formed through phagocytosis and typically follow a particular path through the cell as their contents are digested and broken down by lysosomes so the substances the vacuole contains are then small enough to diffuse through the membrane of the food vacuole into the cell. Anything left in the food vacuole by the time it reaches the cytoproct (anal pore) is discharged by exocytosis. Most ciliates also have one or more prominent contractile vacuoles, which collect water and expel it from the cell to maintain osmotic pressure, or in some function to maintain ionic balance. In some genera, such as Paramecium, these have a distinctive star shape, with each point being a collecting tube.

Mostly, body cilia are arranged in mono- and dikinetids, which respectively include one and two kinetosomes (basal bodies), each of which may support a cilium. These are arranged into rows called kineties, which run from the anterior to posterior of the cell. The body and oral kinetids make up the infraciliature, an organization unique to the ciliates and important in their classification, and include various fibrils and microtubules involved in coordinating the cilia. In some forms there are also body polykinetids, for instance, among the spirotrichs where they generally form bristles called cirri.

The infraciliature is one of the main components of the cell cortex. Others are the alveoli, small vesicles under the cell membrane that are packed against it to form a pellicle maintaining the cell's shape, which varies from flexible and contractile to rigid. Numerous mitochondria and extrusomes are also generally present. The presence of alveoli, the structure of the cilia, the form of mitosis and various other details indicate a close relationship between the ciliates, Apicomplexa, and dinoflagellates. These superficially dissimilar groups make up the alveolates.