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See page Ci. 1 Introduction for more about Ciliophora. (To complete all classifications ETI has added the Kingdom and the Phyla of all the different taxa treated on this DVD-ROM without higher classifications. Texts from Lynn Margulis and Karlene V. Schwartz, Five Kingdoms. CD-ROM Copyright 2002 ETI / Freeman & Co Publishers).
Most ciliates, which are among the best-known protoctists, are bactivorous single cells. Ciliates are characteristically covered with cilia—short undulipodia with kinetosomes embedded in a tough, fibrillar outer cortex (proteinaceous cell layer) of the cell. Like the dinomastigotes (Phylum Dinostigmata) and apicomplexans (Phylum Apicomplexa), ciliates are alveolates, with pits embedded in their cortices. They possess two different types of nuclei, small micronuclei and larger macronuclei, usually more than one of each kind. Nearly 10,000 freshwater and marine species have been described in biology literature. Probably many more exist in nature. Nearly all are phagotrophic, eating bacteria, tissue, or other protists, or they are osmotrophs, utilizing dissolved nutrients in rich waters.
Although ciliates overwhelmingly are single-celled, multicellular slime-mold-like ciliates are known. Sorogena forms a stalked structure from aggregates of cells. It develops propagules, sporelike spheres that germinate into free swimmers, each with its macronucleus and micronucleus.
The cilia of ciliates, like other undulipodia, including sperm tails, have the same ultrastructure, the ninefold symmetrical array of microtubules (the axoneme), with a kinetosome at its base. Cilia are modified to perform specialized locomotory and feeding functions. The most usual modification is the grouping of cilia and their underlying kinetosomes into cirri (bundles) or membranelles (sheets). Cirri or membranelles function as mouths, paddles, teeth, or feet. The ciliate undulipodia are embedded in an outer proteinaceous cell layer (the cortex) about 1 mm thick containing rows of kinetids (the kineties) comprising complex fibrous connections between them. Associated with each kinetid of the ciliate cortex is a parasomal sac, a small invagination of the plasma membrane of unknown function.
Of the two types of nuclei in each ciliate, only the micronuclei, which apparently contain standard chromosomes, divide by mitosis. The huge macronuclei, which develop from precursor micronuclei in a series of complex steps, do not contain typical chromosomes. Instead, the DNA is broken into a great number of little chromatin bodies; each body contains hundreds or even thousands of copies of only one or two genes. Macronuclei are always required for growth and reproduction. They divide by elongating and constricting—not by standard mitosis. They take part in cellular functions such as the production of messenger RNA to direct protein synthesis. The micronuclei, not required for growth or reproduction, are dispensable, essential only for sexual processes unique to ciliates.
Most ciliates reproduce by transverse binary fission, dividing across the short axis of the cell to form two equal offspring. The anterior new cell is called the proter and the posterior one is the opisthe. However, certain stalked and sessile species, such as some suctorians, asexually bud off “larval” offspring. These offspring are “born”: small rounded offspring, covered with cilia, emerge through “birth pores” of their entirely different looking, stalked “mother.”
Most ciliates undergo a sexual process called conjugation. The conjugants, two cells of compatible mating types (“sexes”) remain attached to each other for as long as many hours. Each conjugant retains some micronuclei and donates others to its partner. A series of nuclear fusions, divisions, and disintegrations follows, resulting in the two conjugants becoming “identical twins,” as far as their micronuclei are concerned. The conjugants eventually separate and undergo a complex sequence of maturation steps. Although the micronuclei of the two exconjugants are now genetically identical (each conjugant having contributed equally), each new cell retains the cytoplasm and cortex of only one of the original conjugants. Because cytoplasmic and cortical inheritance in ciliates can be definitively distinguished from nuclear inheritance, these organisms are used in cell genetic analysis.
Ciliate classification has been revised dramatically in the past two decades because of the new information derived from ribosomal RNA sequencing studies and correlated with electron microscopy. “Holotrichs,” ciliates with cilia over the entire surface, are not necessarily related—this formal name has been abandoned. Groups thought to be only very distantly related or unrelated, such as karyorelictans and stentors, are now known to be related, whereas organisms resembling each other superficially, such as Euplotes and Stylonychia, are more distantly related.
The most useful structure for the comparison of ciliates and the reconstruction of evolutionary history is the ciliate kinetid, the structure consisting of one or more kinetosomes and their undulipodia, as well as the ribbons of microtubules and filaments, including kinetodesmal fibers, that surround them. Kinetids are universal units of structure in all protoctist, animal, and plant cells that bear undulipodia. A kinetid with a single kinetosome is called a monokinetid, that with two kinetosomes is a dikinetid, and the rarer kinetid with many is called a polykinetid.
On the basis of kinetid structure and organization, the ciliates are divisible into three subphyla: Postciliodesmatophora, a group of ciliates with dikinetids, contains two classes: Karyorelictea and Spirotrichea. Heterotrichs, including Stentor and Gastrostyla (illustrated here) belong in this subphylum. The subphylum Rhabdophora, ciliates that have kinetids with short kinetodesmal fibers and tangential transverse ribbons of microtubules, contains two classes: Prostomea and Litostomea. Among many others, entodiniomorphs, bizarre-looking ciliates living as symbionts in the mammalian rumen, are classified in Litostomea. The third subphylum, Cyrtophora, contains four classes: Nassophorea, Phyllopharyngea, Colpodea, and Oligohymenophora. The cyrtophoran, unlike the rhadophoran, disassembles its complex oral ciliature and makes two new ones in the process of cell division. Nearly all the well-known ciliates—Colpoda (Class Colpodea: Subclass Colpodida), Tetrahymena (Class Oligohymenophora: Subclass Scuticociliatida), Vorticella (Class Oligohymenophora: Subclass Peritrichia), Paramecium (Class Nassophorea: Subclass Peniculida), and Stylonychia, Oxytricha, and Pleurotricha (Class Nassophorea: Subclass Hypotrichia), as well as the subclass Suctoria (Class Phyllopharyngea), belong in this great subphylum of ciliates.
Although many form spherical, resistant cysts, most ciliates lack hard parts and therefore do not fossilize. The tintinnids, heterotrichs in Subphylum Postciliodesmatophora, are exceptional marine ciliates that make shell-like structures from sand and organic cements. Their ancestors left evidence in the fossil record that they evolved before the Cretaceous period, some 100 million years ago.
Because of their various ciliary modifications, their rapid and controllable growth rates, and the ease with which they can be handled in the laboratory, ciliates are valuable for anatomical, genetic, and neurophysiological studies of single cells. Except for the parasite Balantidium, which occasionally grows in the human gut, ciliates cause no disease and are of little immediate economic importance.

Outline classification
The following is according to the Chapter Ciliophora as published in South Atlantic Zooplankton. There is no commonly accepted classification scheme for ciliates. The following, rather conservative system is an abridged version based on that given by Corliss (1979), centered on representatives from the South Atlantic Ocean and with some minor additions by Foissner and Foissner (1988) and Petz and Foissner (1992). Taxa in bold characters are those treated in detail in this chapter.

Kingdom Protoctista Hogg, 1861
Phylum Ciliophora Doflein, 1901
Class Kinetofragminophora de Puytorac et al., 1974
Subclass Gymnostomata Bütschli, 1889
Order Primociliatida Corliss, 1974
Order Karyorelictida Corliss, 1974
Family Trachelocercidae Kent, 1881
Family Loxodidae Bütschli, 1889
Family Geleiidae Kahl, 1933
Family Protocruziidae Jankowski, 1980
Order Prostomatida Schewiakoff, 1896
Suborder Prostomatina Schewiakoff, 1896
Suborder Prorodontina Corliss, 1974
Family Prorodontidae Kent, 1881
Family Colepidae Ehrenberg, 1838
Order Gymnostomatida Bütschli, 1889
Order Spathidiida Foissner and Foissner, 1988
Suborder Spathidiina Jankowski, 1980
Family Spathidiidae Kahl in Doflein and Reichenow, 1929
Family Trachelophyllidae Kent, 1882
Family Lacrymariidae Fromentel, 1876
Family Homalozoonidae Jankowski, 1980
Suborder Belonophryina Jankowski, 1980
Suborder Didiniina Jankowski, 1978
Family Didiniidae Poche, 1913
Order Pleurostomatida Schewiakoff, 1896
Suborder Amphileptina Jankowski, 1967
Suborder Litonotina Foissner and Foissner, 1988
Family Litonotidae Kent, 1882
Family Loxophyllidae Foissner and Leipe, 1995
Order Pseudoholophryida Foissner and Foissner, 1988
Order Cyclotrichida Jankowski, 1980
Family Mesodiniidae Jankowski, 1980
Order Archistomatida de Puytorac et al., 1974
Subclass Vestibulifera de Puytorac et al., 1974
Order Trichostomatida Bütschli, 1889
Suborder Trichostomatina Bütschli, 1889
Family Plagiopylidae Schewiakoff, 1896
Family Coelosomididae Corliss, 1961
Family Trichospiridae Kahl, 1926
Family Trimyemidae Kahl, 1933
Family Marynidae Poche, 1913
Family Balantidiidae Reichenow in Doflein and Reichenow, 1929
Family Pycnotrichidae Poche, 1913
Family Isotrichidae Bütschli, 1889
Family Paraisotrichidae da Cunha, 1917
Family Protocaviellidae Grain in Corliss, 1979
Suborder Blepharocorythina Wolska, 1971
Order Entodiniomorphida Reichenow in Doflein and Reichenow, 1929
Order Colpodida de Puytorac et al., 1974
Subclass Hypostomata Schewiakoff, 1896
Order Synhymeniida de Puytorac et al., 1974
Order Nassulida Jankowski, 1967
Order Cyrtophorida Fauré-Fremiet in Corliss, 1956
Suborder Chlamydodontina Deroux, 1976
Family Chilodonellidae Deroux, 1970
Family Chlamydodontidae Stein, 1859
Family Lynchellidae Jankowski, 1968
Suborder Dysteriina Deroux, 1976
Family Plesiotrichopidae Deroux, 1976
Family Hartmannulidae Poche, 1913
Family Dysteriidae Claparède and Lachmann, 1858

Incerta sedis
Family Kryoprorodontidae Alekperov and Mamaeva, 1992
Suborder Hypocomatina Deroux, 1976
Order Chonotrichida Wallengren, 1895
Order Rhynchodida Chatton and Lwoff, 1939
Order Apostomatida Chatton and Lwoff, 1928
Subclass Suctoria Claparède and Lachmann, 1858
Order Suctorida Claparède and Lachmann, 1858
Suborder Exogenina Collin, 1912
Family Podophryidae Haeckel, 1866
Family Parapodophryidae Jankowski, 1973
Family Urnulidae Fraipont, 1878
Family Ephelotidae Kent, 1882
Family Spelaeophryidae Jankowski in Batisse, 1975
Family Rhabdophryidae Jankowski, 1970
Family Stylostomatidae Batisse, 1975
Family Ophryodendridae Stein, 1867
Family Tachyblastonidae Grell, 1950
Family Thecacinetidae Matthes, 1956
Family Phalacrocleptidae Kozloff, 1966
Suborder Endogenina Collin, 1912
Family Acinetidae Stein, 1859
Family Dendrosomatidae Fraipont, 1878
Family Trichophryidae Fraipont, 1878
Family Endosphaeridae Jankowski in Corliss, 1979
Suborder Evaginogenina Jankowski in Corliss, 1979
Class Oligohymenophora de Puytorac et al., 1974
Subclass Hymenostomata Delage and Hérouard, 1896
Order Hymenostomatida Delage and Hérouard, 1896
Order Scuticociliatida Small, 1967
Suborder Philasterina Small, 1967
Family Philasteridae Kahl, 1931
Family Uronematidae Thompson, 1964
Family Cohnilembidae Kahl, 1933
Family Entorhipidiidae Madsen, 1931
Family Entodiscidae Jankowski, 1973
Family Cryptochilidae Berger in Corliss, 1979
Family Thyrophylacidae Berger in Corliss, 1961
Family Loxocephalidae Jankowski, 1964
Family Cinetochilidae Perty, 1852
Family Urozonidae Grolière, 1975
Family Pseudocohnilembidae Evans and Thompson, 1964
Family Thigmophryidae Chatton and Lwoff, 1926
Suborder Pleuronematina Fauré-Fremiet in Corliss, 1956
Family Pleuronematidae Kent, 1881
Family Cyclidiidae Ehrenberg, 1838
Family Histiobalantidae de Puytorac and Corliss in Corliss, 1979
Family Peniculistomatidae Fenchel, 1965
Family Thigmocomidae Kazubski, 1958
Family Conchophthiridae Kahl in Doflein and Reichenow, 1929
Suborder Thigmotrichina Chatton and Lwoff, 1922
Order Astomatida Schewiakoff, 1896
Subclass Peritricha Stein, 1859
Order Peritrichida Stein, 1859
Suborder Sessilina Kahl, 1933
Family Vorticellidae Ehrenberg, 1838
Family Astylozoidae Kahl, 1935
Family Epistylididae Kahl, 1933
Family Operculariidae Fauré-Fremiet in Corliss, 1979
Family Opisthonectidae Foissner, 1976
Family Scyphididae Kahl, 1933
Family Ophrydiidae Ehrenberg, 1838
Family Ellobiophryidae Chatton and Lwoff, 1929
Family Termitophryidae Lom in Corliss, 1979
Family Rovinjellidae Matthes, 1972
Family Vaginicolidae Fromentel, 1874
Family Lagenophryidae Bütschli, 1889
Suborder Mobilina Kahl, 1933
Class Polyhymenophora Jankowski, 1967
Subclass Spirotricha Bütschli, 1889
Order Heterotrichida Stein, 1859
Suborder Heterotrichina Stein, 1859
Family Spirostomidae Stein, 1867
Family Phacodinidae Corliss, 1979
Family Metopidae Kahl, 1927
Family Condylostomatidae Kahl in Doflein and Reichenow, 1929
Family Reichenowellidae Kahl, 1932
Family Climacostomatidae Repak, 1972
Family Stentoridae Carus, 1863
Family Bursariidae Dujardin, 1840
Family Chattonidiidae Villeneuve-Brachon, 1940
Family Peritromidae Stein, 1867
Suborder Clevelandellina de Puytorac and Grain, 1976
Suborder Armophorina Jankowski, 1964
Suborder Colinophorina Jankowski, 1967
Suborder Plagiotomina Albaret, 1974
Suborder Licnophorina Corliss, 1957
Family Licnophoridae Bütschli, 1887
Order Odontostomatida Sawaya, 1940
Order Oligotrichida Bütschli, 1887
Order Hypotrichida Stein, 1859
Suborder Stichotrichina Fauré-Fremiet, 1961
Family Spirofilidae Gelei, 1929
Family Strongylidiidae Fauré-Fremiet, 1961
Family Urostylidae Bütschli, 1889
Family Psilotrichidae Bütschli, 1889
Family Kiitrichidae Nozawa, 1941
Family Keronidae Dujardin, 1840
Suborder Sporadotrichina Fauré-Fremiet, 1961
Family Oxytrichidae Ehrenberg, 1838
Family Aspidiscidae Ehrenberg, 1838
Family Euplotidae Ehrenberg, 1838
Family Gastrocirrhidae Fauré-Fremiet, 1961

A phylogenetic approach using morphologic and morphogenetic characters resulted in a considerably different system for aloricate oligotrichs (Petz and Foissner, 1992). As this group dominates the ciliate fraction in the marine plankton, this improved scheme is given below. Apomorphies showed that strombidiids are more closely related to tintinnids and strobilidiids than to halteriids, which makes the recently proposed order Choreotrichida Small and Lynn, 1985 superfluous. It also followed from that study that the hypotrichs should be elevated to class rank as later proposed by Tuffrau and Fleury (1994).

Class Oligotrichea Bütschli, 1887
Subclass Halteriia Petz and Foissner, 1992
Order Halteriida Petz and Foissner, 1992
Family Halteriidae Claparède and Lachmann, 1858
Subclass Oligotrichia Bütschli, 1887
Order Strombidiida Jankowski, 1980
Family Strombidiidae Fauré-Fremiet, 1970
Order Oligotrichida Bütschli, 1887
Suborder Strobilidiina Jankowski, 1980
Family Strobilidiidae Kahl in Doflein and Reichenow, 1929
Suborder Strombidinopsina Small and Lynn, 1985
Family Strombidinopsidae Small and Lynn, 1985
Suborder Tintinnina Kofoid and Campbell, 1929

Phylum Ciliophora