Classification schemes have been as diverse as the organisms they try to classify. Even older schemes, based entirely on light microscopy, recognized some groups as practical rather than natural. Newer schemes add structures visible via electron microscopy plus a better understanding of physiology, genetics, biochemistry and molecular biology.

Kozloff uses the traditional classification put together by a committee of protozoologists:

• Sarcomastigophora
• Mastigophora (flagellates)
• Phytomastigophorea (chiefly phototrophic flagellates)
• Zoomastigophorea (chiefly heterotrophic flagellates)
• Sarcodina (amoebas, foraminiferans, radiolarians, &c.)
• Apicomplexa, Microspora, Myxozoa (3 entirely parasitic groups formerly placed together as "Sporozoa")
• Ciliophora (ciliates)
• Opalinata (formerly variously considered a flagellate or ciliate)

Considered among the most primitive eukaryotes, or at least those that diverged earliest among the Eucarya. As a result, they have sometimes been placed together in a single group called the Archezoa. However, no features link these groups beyond their common, apparently plesiomorphic lack of mitochondria, and recent research suggests that the mitochondria have been secondary lost. Several other groups not discussed here (e.g., retortamonads, oxymonads) were formerly grouped together with the parabasalids and diplomonads among the zoomastigophorans, the "animal flagellates".

1. PARABASALIA

• Heterotrophic endosymbionts
• Several to many anterior flagella
• Parabasal structures consisting of complexes of flagellar basal body fibres, golgi apparatuses, and microtubules; associated with some flagellar basal bodies
• Cell wall and pellicle absent
• Store glycogen

• Usually 4-6 flagella with one adhering to an undulating membrane
• One to many nuclei (each with a group of associated flagella)
• Various microtubular structures (e.g., pelta, axostyle)
• Trichomonas vaginalis: parasite of human reproductive organs

• Many flagella in straight or spiral rows
• One nucleus
• Endosymbionts in wood-digesting roach and termite guts. They phagocytize wood particles and digest cellulose via endobiotic bacteria

• Heterotrophic symbionts and free-living species
• Paired nuclei associated with paired axostyles and  pair of clusters of 1-4 flagella, one of which lies along the cell body
• Giardia lamblia is an important human gut parasite

• Cylindrical, freshwater amoebas formerly considered as lobose rhizopods
• Symbiotic bacteria function in place of mitochondria
• Non-motile surface extensions similar to flagella
• Nuclear division amitotic
• NOTE: Placement here is tentative (the mitochondria may have been secondarily lost)

• Minute unicellular parasites causing single-cell tumors in a great variety of insects and other animals
• "Spores" invade host cells via a polar tube that does not damage the host cell membrane
• Cell fusion reported for some species
• The most recent information suggests a closer relationship with fungi.

Mereschkowsky first suggested in 1905 that mitochondria derived from bacteria, and Margulis revived the hypothesis in 1970. Comparisons of ribosomal RNA and other molecules have since confirmed the idea. The current hypothesis holds that mitochondria originated as endosymbionts, most likely one group of "purple bacteria", and that the relationship arose once, making possession of mitochondria a synapomorphy identifying a  mitochondriate eukaryote clade. Precise phylogenetic relationships among many of the groups are still unclear. However, most traditional groups such as the phytomastigophorans (plantlike flagellates), sarcodines, actinopods and radiolarians have been broken up and are no longer recognized as coherent, monophyletic groups.

5. EUGLENOZOA

• One or more flagella arise from a reservoir depression
• Flagellum thickened by a paraxial rod composed of protein complexes parallel to the 9+2 microtubules
• Microtubular ribbons stiffen the cell cortex (outer layer) and generate a relatively constant cell shape

• Photo- and heterotrophic, chiefly freshwater flagellates
• Two or more flagella (usually 1-2 emergent)
• Chlorophyll a and b
• Storage product paramylon (a polysaccharide)
• Longitudinal microtubules permit euglenoid movement
• Mitosis without spindle; nuclear membrane remains intact
• Stigma (eyespot) of carotenoid grains probably acts as shield for a tiny photoreceptor

• Heterotrophic, free-living and parasitic flagellates
• One emergent flagellum usually attached along an undulatory membrane
• Large mitochondrion (tube, hoop or branching network) with a DNA-containing kinetoplast
• Trypanosoma causes sleeping sickness (vector: Tsetse fly), Chagas disease (vector: biting reduviid bugs; bug feces contaminate bite wound).
• Leishmania causes Kala-azar; affects, marrow, spleen, skin, mucous membranes, &c. (vector: sand flies)

A variety of free-living and parasitic amoebas, together with some slime molds and the amitochondriate Pelomyxa were formerly classified together as the Rhizopoda. Unpublished RNA data scatters them polyphyletically across the Protoctista.

• Single-celled amoebas lacking flagella or centrioles

• Marine, freshwater and terrestrial
• Naked (e.g., Amoeba) or testate (shelled) (e.g., Arcella, Difflugia)
• Pseudopods are lobate or tubelike (lobopods)
• Meiosis and sexual reproduction absent
• Reproduction via asexual fission

• Slender, filamentous or fine branching pseudopods (filopods) with microfilamentous axes (e.g., Euglypha)

• Endosymbiotic, parasitic and coprozoic forms
• Entamoeba histolytica causes amoebic dysentery; produces severe intestinal ulceration and diarrhea; contracted via ingestion of encysted stages

• A polyphyletic group of amoeboid forms with axopodia: pseudopods with an internal skeleton of microtubules
• Spherical or radial symmetry
• Most have an inorganic skeleton
• First three groups formerly considered together as Radiolaria

• Marine planktic
• Silica skeleton of needles or perforated globes; fossil record dates to Precambrian Era
• Distinct mucoprotein central capsule separates dense, nucleated endoplasm from ectoplasm
• Axopods with complex microtubular arrays arise in endoplasm and penetrate central capsule via pores
• Ectoplasm often with endosymbiotic zooxanthellae or zoochlorellae (green algae)
• Some colonial species with numerous capsules in gelatinous mass up to 30 cm long

• Marine deep-water planktic
• Chiefly hollow skeleton of amorphous silica, organic material and trace metals
• Central capsule with three pores
• Algal symbionts absent
• Nuclear division resembles mitosis but with hundreds of chromosomes

• Marine planktic
• Radiating skeleton of 10 or 20 SrSO₄ (strontium sulfate) rods joined at center
• Central endoplasm with numerous nuclei and often zooxanthellae
• Life cycles include cysts and flagellated swarmers

• Marine, freshwater and semiterrestrial in sphagnum moss
• Formerly included with several other groups in the Heliozoea, the sun animalcules, now considered polyphyletic
• Axopodial microtubules arranged in a double spiral
• Unique form of autogamy (self-fertilization) in which an encysted mother cell divides into two gametes that then fuse

• Finely granular pseudopods form anastomosing networks (reticulopods)

• Perforated organic tests, usually multichambered, reinforced with CaCO₃ or cemented mineral grains
• Sexual reproduction with meiosis and alternation of adult diploid and smaller haploid generations; no eggs or sperm
• Chiefly marine, benthic (~4000 species) and planktic (~150 species)
• Some have zooxanthellae
• Tests of planktic species (e.g., Globigerina, Globorotalia) form extensive abyssal sediments (foram ooze).
• Important nanofossils (~30,000 species), including important indicators of paleoclimates.
• The Egyptian pyramids were built of Eocene sandstone dominated by coin-sized Nummulites.

• Deep sea amoeboid forms up to 27 cm across
• Cytoplasm contains barite crystals and many nuclei in a branched tube system of clear organic material
• Foreign material (e.g., sediment grains, sponge spicules) aggregates around tube system
• Fecal material retained externally

• Chiefly marine, single-celled phototrophs; important nanoplankton
• Motile stage with two nonhairy flagella
• Filamentous (sometimes stumplike or reduced) haptonema with a core of 6-8 microtubules enveloped by endoplasmic reticulum; used for attachment, locomotion and food capture
• Yellow xanthophylls mask chlorophyll a and c
• Storage is chrysolaminarin or paramylon
• Cell body covered by cellulose-containing, organic scales
• Scales often calcified (coccoliths) in nonmotile stages; important nanofossils

• Green algae and their descendants including land plants
• Phototrophs containing chlorophylls a and b
• Storage is starch, stored inside double-membrane-bounded chloroplasts
• Cell walls of cellulose

• Chiefly freshwater
• Two to eight anterior smooth flagella
• Cup-shaped chloroplast
• Single-celled (e.g., Chlamydomonas) or colonial (Volvox, Pandorina)
• Colonial forms have cells imbedded in common gelatinous matrix, often connected by cellular projections
• Zoochlorellae are unicellular green algae endosymbiotic in other organisms (e.g., ciliates)

Includes three major "protozoan" groups that, traditionally, were never considered closely related: the dinoflagellates, ciliates and apicomplexan sporozoans. The following features that they have in common had to await electron microscopy and molecular biology before they could be discovered:

• Flattened membrane-bound sacs (cortical alveoli) just beneath the cell membrane (part of the pellicle)
• Longitudinally arranged microtubules below the alveoli
• Extrusomes (also called trichocysts, rhoptries, micronemes, haplosporosomes): organelles used for prey capture in ciliates and dinoflagellates, and for modification of the intracellular space in apicomplexans
• Tubular mitochondrial cristae (characteristic of but not unique to this group)
• Similarities among small and large subunit ribosomal DNA (rDNA) sequences (molecular data confirm morphological similarities)

• One ribbonlike, undulatory flagellum located in an equatorial or spiral groove (annulus); maintains cell orientation.
• One whiplash flagellum trails in posterior groove (sulcus); provides propulsion.
• Unique nuclei with chromosomes condensed throughout cell cycle and nuclear membrane intact during mitosis.
• Chiefly haploid; sexual reproduction known.
• Phototrophic species have chlorophyll a and c masked by peridinin (a xanthophyll).
• Storage products starch and oil.
• Chiefly single-celled and marine, important components of the phytoplankton; some colonies
• Photo- and heterotrophic, benthic and planktic species; motile and nonmotile stages; free-living and symbiotic (including parasitic)
• Many luminescent species (Bahias foforentes)
• Armored, or thecate, species appear to have the cell surface divided into a series of "armor plates"; the hardened theca is  a dense proteinaceous material deposited inside the alveoli.
• Toxin-producing planktonic forms (e.g., Gonyaulax, Gymnodinium) may occur in blooms (huge and abrupt populations increases) called red tides apparently generated by large-scale nutrient inputs (e.g., upwelling or run-off).
• Eating bivalve mollusks that have concentrated toxic dinoflagellates causes paralytic shellfish poisoning (thus, avoid eating bivalves in months lacking "r" in their name).
• Toxic benthic species are probably responsible for ciguatera, a chronic nervous system syndrome caused by eating fish in which toxins have been bioconcentrated.
• Zooxanthellae are endosymbiotic phototrophic dinoflagellates (Symbiodinium) found in Cnidaria, mollusks, actinopods, foraminiferans, flatworms that contribute to their host's nutrition.
• Heterotrophic fish ectoparasites with rootlike penetration processes; their dispersal stage is a typical dinoflagellate.
• Noctiluca is a large (to 1.5 mm), luminescent, spherical planktic species with a short flagellum and a thick adhesive tentacle for food capture. It incorporates low-density NH₄⁺ salts to increase buoyancy.

• All or partly covered with cilia identical in fine structure to eukaryote flagella
• Complex infraciliature of units called kinetids composed of basal bodies (kinetosomes) and rootlets (kinetodesmal fibrils and microtubules)
• Macro- and micronuclei (latter divide by mitosis)
• Permanent oral and anal openings
• Asexual reproduction via transverse fission
• Conjugation, a unique sexual reproduction in which two cells fuse temporarily and exchange micronuclei.
• Chiefly single-celled and heterotrophic
• Benthic and planktic; marine, freshwater and soil-dwelling, including extreme environments such as Antarctic ice and hot springs

• Chiefly slender, elongated and contractile, marine interstitial species
• Macronuclei degenerate before mitosis and are restored afterwards by an additional fission of the micronucleus

• Often very large species, to 2 mm long; marine and freshwater
• Extensive right-winding oral membranelles
• Often contractile and brightly pigmented (contractile system differs from actomyosin)

• Chiefly marine planktic; important bacterivores in marine food webs
• Cilia largely restricted to well-developed oral membranelles for feeding and locomotion
• Cytoproct absent; many species are semi-autotrophic or mixotrophic via cultivation of chloroplasts from ingested algae
• One subgroup, the tintinnids, produce a protective organic lorica that incorporates foreign particles (e.g., sediment grains, coccoliths); they have a fossil record dating to the Ordovician

• Typically flattened ciliates with oral membranelles and ventral locomotor cirri (fused cilia)

• Mainly predatory forms with microtubular bundles that strengthen the cytostome
• Extrusive toxicysts present

• Endosymbionts in animal intestines, including ruminants; endobiotic bacteria permit digestion of cellulose
• Cilia dense around cytostome, reduced to zones on body
• Often bizarre body shapes stabilized by a conspicuous layer of microfilaments
• Cytological differentiation sometimes extreme
• Mitochondria lost, replaced by hydrogenosomes (H₂ generation)

• Chiefly freshwater, often stalked, aberrant predators on ciliates and other suctorians
• Adults lack cilia; swarmers budded from mother cells have cilia
• Knob-tipped feeding tentacles pierce prey cells; prey is "sucked" into tentacles via microtubule activity

• Oral apparatus consists of a small elastic slit surrounded by a complex of small membranelles

• Oral membranelles in wreath around oral end, which can contract and withdraw
• Reduced body cilia
• Most stalked, some colonial, some loricate
• Often ectosymbionts on marine and freshwater invertebrates

• Heterotrophic, obligate endoparasites of animals
• Apical complex of microtubular structures and bottle-shaped extrusomes (rhoptries) involved in penetration of or attachment to host
• Intricate life cycles involve sexual and asexual reproduction with alternation of diploid and haploid generations

• Chiefly extracellular parasites in intestines and body cavities of arthropods (and some other invertebrates)
• Feeding gamonts (gamete-producing stages) attach to their host epithelium via a modified portion of the apical complex (conoid) and may reach 10 mm in length
• Both male and female gamonts undergo multiple fission and produce similar numbers of gametes
• In many species, male and female gamonts mate before completing growth and then encyst together

• Endoparasites with an obligatory alternation between the blood of intermediate vertebrate hosts and the gut and body cavity of final arthropod hosts
• Apical complex reduced
• In malaria (Plasmodium spp.), cells injected by mosquitos invade vertebrate liver cells and develop into large (1 mm) schizonts which divide by multiple asexual fission (schizogony) into thousands (up to 20,000) of merozoites that are released into the bloodstream
• Merozoites invade erythrocytes (red blood cells) and undergo further schizogony, producing more merozoites
• Merozoites ingest hemoglobin via phagocytosis and ultimate cause the erythrocytes to lyse
• Synchronous release of merozoites from erythrocytes produces cell fragments and pigment bodies that cause periodic fever and other symptoms
• After about 10 days, some merozoites develop into male and female gamonts
• After ingestion with a mosquito's blood meal, gamonts produce micro- and macrogametes in the insect's intestine
• Fertilization occurs in the intestine and the motile zygote (ookinete) invades the intestine wall and is encapsulated
• The encapsulated ookinete undergoes multiple asexual divisions (sporogony) to produce large numbers of slender sporozoites
• Sporozoites become infective agents after bursting out of the capsule and migrating via the hemolymph to the mosquito's salivary glands, to await injection again
• Four species of Plasmodium cause malaria in humans; +200 million people probably suffer from symptoms of pernicious malaria worldwide; the World Health Organization estimates that a million malarial-infected children die in Africa alone yearly

• Intracellular parasites
• Macrogamonts do not divide, but develop directly into oocytes
• Cryptosporidium is a significant cause of diarrheal disease in animals and humans
• Toxoplasma invades cats as final hosts; humans may be infected as intermediate hosts via cat feces or raw meat; pathological symptoms include lymph node diseases and, via infection of pregnant women, severe or fatal toxoplasmosis of the fetus

• Mastigonemes (hairs on flagella) tubular, tripartite and formed from Golgi vesicles (lost in some groups, e.g., diatoms)

• One of several groups of phototrophic flagellates formerly grouped in the Chrysophyta ("golden algae"), now considered polyphyletic
• Single flagellum and many slender pseudopods
• Star-shaped silica skeleton; important nanoplankton (and nanofossils)
• Chlorophylls a and c masked by fucoxanthin
• Storage chrysolaminarin and lipids

• Nonparasitic endocommensals in the terminal part of the intestine of frogs, some fish and a few reptiles
• Multinucleate, usually flattened and large (up to 3 mm)
• Covered with thousands of relatively short cilia-like flagella (infraciliature and alveoli absent), arising from a group of anterior flagellar rows; arranged in helical rows and beating in metachronal waves
• Folds in cell surface supported by microtubules
• No cytopharynx; nutrients absorbed via pinocytosis over entire cell surface
• Complex life histories in which cells released from cysts may develop into normal commensals or sexual stages
• Different former classifications placed them among ciliates, flagellates, or as an independent group

• Chiefly marine coastal and estuarine; sometimes freshwater or in saline soils
• Mostly associated with algae or plant detritus, or detrital sediments
• Typical feeding stage consists of a wandering plasmodium (large multinucleate cell) up to several cm across
• Spindle-shaped cell-like bodies glide within an ectoplasmic network of pseudopod-like tubes; the gliding mechanism is unknown
• Double-membraned cell bodies have special openings to the surrounding ectoplasm which, in turn, is surrounded by a common cell membrane
• Sexual reproduction involves multicellular cysts, sporangia and flagellated swarmer zoospores with a pigmented eyespot
• Implicated in some seagrass diseases

• Small, heterotrophic, uninucleate single sessile cells or planktic colonies; marine or freshwater
• Anterior basket-like collar of slender microvilli surround a single flagellum
• Often with membranous sheath or siliceous lorica
• Important bacterivorous nanoplankton
• Collars, ability to metabolize silica and discharge of osmotic water via contractile vacuoles are also found in sponge choanocytes, suggesting a possibly close phylogenetic relationship with sponges

Barnes, R.S.K. 1984. A Synoptic Classification of Living Organisms. Sinauer, Sunderland, MA. 273 pp.

Corliss, J. O. 1984. The Protista Kingdom and its 45 Phyla. Biosystems 17:87-126.

Hausmann, K. & Hulsmann, N. 1996. Protozoology (2nd ed.). Georg Thieme Verlag, Stuttgart. 338 p.

Margulis, L. & Schwartz, K.V. 1988. Five Kingdoms. (2nd ed.) Freeman, NY. 376 pp.

Zettler, L. A., Sogin, M.L. and Caron, D. A. 1997. Phylogenetic relationships between the Acantharea and the
Polycystinea: A molecular perspective on Haeckel's Radiolaria. Proceedings of the National Academy of Sciences, USA 94:11411-11416.
 
 

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