The ciliates consist of a diverse phylum with >250 families of free-living species, in ten classes. Although common in the soil habitats, only one class is abundant in soil samples, while species in other families are active in small numbers only (Foissner, 1987) (Fig. 1.18). In general, cili-ates are characterized by two functionally distinct nuclei and the presence of alveolar membranes under the cell membrane, long tubular cristae, extrusomes that are defensive or for predation, pluri-ciliated trophic or dispersal stages, cilia basal bodies organized into a coordinated system and a coated pit (parasomal sac) adjacent to cilia. The two nuclei are distinguished as the micronucleus which is inactive but participates in mitosis and meiosis, and the macronucleus which is polyge-nomic (with amplified copy number of the active genes). The macronucleus in most classes loses some or all transcriptionally inactive genes in the vegetative phase. The alveolar membranes were demonstrated to store calcium in some species. The extrusomes may secrete defensive mucus (mucocyst) which sometimes has degradative enzymes or toxins. Alternatively, they may be trichocysts, which discharge a lance into prey or predator. The somatic and cytostome ciliature is key to identification and requires silver staining or electron microscopy, espe-
Fig. 1.18. Representative soil ciliates. (A) The fungivorous Pseudoplatyophrya (Grossglockneriididae, Colpodea). (B) A bacterivorous Spathidium (Spathidiidae, Litostomatea). (C) The cytotrophic Bresslaua (Colpodidae, Colpodea). (D) The omnivorous Sterkiella (Oxytrichidae, Stichotrichia). Scale bar (A and B) 25 ^m, (C and D) 50 ^m.
cially for the smaller species (Foissner, 1991; Lynn, 1991; Lynn and Small, 2002). Details of the ultrastructure of the kinetids are essential in family and genus identification. The kinetosome are arranged as single or paired somatic basal bodies. Not all carry a cilium. They are linked by cytoskeletal elements in longitudinal rows and beat in chronological sequence. The kinetosomes may be grouped in clusters of synchronously beating cilia. Most soil Ciliophora have a cytostome, specialized for the accumulation or apprehension of food particles by phagotrophy. The cytostome has specialized cilia and a shape which varies between families and genera. Some endosymbionts have lost the cytostome and feed by osmotrophy and pinocytosis. Others, such as several sand ciliates (Kentrophoros, Trachelonema and Tracheloraphis), do not have a cytostome, but phagocytosis occurs over a part of the somatic cell membrane. Many species are known to have endosymbiotic bacteria or protists. Ciliates are often sexual species, with two or many complementary mating types able to conjugate.
Contrary to the claim of early protozoologists, species found in marine sediments, soil and fresh water are distinct and habitat restricted. However, many edaphic species can be sampled from fresh water, especially as cysts, through surface runoff and leaching of water from the soil to streams. Particular adaptations of soil species are cysts resistant to desiccation (sometimes for decades), thigmotactic or surface-associated feeding, and a flexible and somewhat labile shape in thin water films. In general, about 50% of soil species are Colpodea and 37% are surface-associated Stichotrichia (Foissner, 1987).
The class Karyorelictea occurs in intertidal and marine sands, where most species feed on bacteria, although some are cytotrophic. Other ciliate taxa also occur in this habitat. Some species are associated with ectosymbiont bacteria, such as the sulphur bacteria on Kentrophoros. An extensive treatment of these intertidal species is provided in Dragesco (1960). The hypotrich subclass Stichotrichia contains many soil species, particularly in the family Oxytrichidae. Most are bacterivorous or cytotrophic on small protists, and many have a range of prey choice. Several species are known to change cell length and dimensions dramatically with changing resources, as well as changing preferred prey. Certain families across ciliates may appear in anaerobic water-saturated soil, such as species in the orders Armophorida and Odontostomatida. The class Litostomatea contains cytotrophic and predacious species which may be encountered occasionally. In surface litter during wet periods, Vorticellidae (Peritrichia) may occur in abundance. They are stalked ciliates that feed on bacteria by filter feeding. Gut endosymbionts of invertebrate saprotrophs (centipedes, millipedes, insects and oligochaetes) occur in the order Clevelandellida. The subclass Astomatia contains families that are endosymbionts (or parasitic) of annelid guts, particularly in oligochaetes and other invertebrate taxa. The class Colpodea are primarily soil species and are the more usually encountered ciliates in the soil. There are six orders with 12 families (Foissner, 1993; Lynn and Small, 2002). Cell division occurs inside cysts in the Bryophryida and Colpodida. Most species of Colpodea are bacterivorous, but some with larger cytostome are known to be cytotrophic, such as Bresslaua (Colpodidae). The Grossglockneriididae (Colpodida) are small species of 10-15 ^m which puncture hyphae and yeast cell walls with an extensible cytostome to ingest the cytoplasm. The single genus of the Sorogenida is unusual, in forming cell aggregates which form a soro-carp reminiscent of the Dictyosteliida (Ameobozoa), and for feeding on other colpodids.
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