175 Abstract The Class ARMOPHOREA represents a new assemblage of ciliates, and one of the two “ riboclasses” as their establishment is completely dependent upon small subunit rRNA gene sequences that showed affi nities of the two included orders – Armophorida and Clevelandellida. The ciliates in this class occupy anoxic habitats. Armophorids are typical of sapropelic habitats, but can be benthic or planktonic, while clevelandellids are endosymbi- onts in the digestive systems of a wide variety of invertebrates, particularly insects, and some verte- brates, particularly amphibians. While their somatic dikinetids are quite different, armophoreans are all characterized by having their mitochondria trans- formed to hydrogenosomes, organelles that provide hydrogen to the methanogenic bacterial symbionts of these ciliates. The oral structures of the two orders are also divergent: membranelle-like in armophorids and heteromembranelles in clevelandellids. Stomato- genesis is pleurotelokinetal. The macronucleus is of simple form, but polytene chromosomes develop after conjugation and the macronuclear DNA ulti- mately differentiates into gene-sized pieces. Armo- phorids, because of their habitat preferences, are particularly good bioindicators of anoxic aquatic environments. Keywords Endosymbiont, cathetodesmal fi bril, sulfureta, secant system The ciliates included in this class are typically small to medium-sized cells. Armophoreans are free- swimming and typically holotrichously ciliated. However, their body ciliation can vary from many, densely ciliated kineties in some clevelandellids to only anterior and posterior cirrus-like tufts in some armophorids. All species have multiple adoral polykinetids, ranging from around a dozen in some armophorids to several dozens in some clevelandellids . These ciliates are very restricted in their distribution. Although world-wide, they are confined to sediments, both aquatic (Fenchel, 1993) and terrestrial (Foissner, 1987), and the water column (Fenchel et al., 1995), where oxygen tensions are extremely reduced to absent. They are also found as endocommensal symbionts in the digestive tracts of a variety of metazoans, rang- ing from selected invertebrates (Albaret, 1970b; Hackstein & Stumm, 1994) through to amphibians (Affa’a, Ndongo, & Granosik, 1995). Interest has increased in the group recently because they harbor endosymbiotic methanogenic bacteria , which can themselves produce the greenhouse gas, methane . There can be thousands of methanogenic bacteria per ciliate (van Bruggen, Stumm, & Vogels, 1983), producing significant quantities of methane , which is then liberated into the environment (Fenchel & Finlay, 1992; Hackstein & Stumm, 1994). The name of the class, ARMOPHOREA , is derived from the subordinal name originally pro- posed by Jankowski (1964a, 1964b) to include only the caenomorphid heterotrichs, which he argued derived from a Metopus -like ancestor. It derives from the Latin arma , meaning weapons (or it derives from the Latin armus meaning shoulder), and refers to the fact that caenomorphids have the appearance of military helmets (or the caenomor- phid body is twisted to give the appearance of a shoulder). Although not highly similar, a number Chapter 8 Subphylum 2. INTRAMACRONUCLEATA: Class 2. ARMOPHOREA – Sapropelibionts that Once Were Heterotrichs 176 8. Subphylum 2. INTRAMACRONUCLEATA: Class 2. ARMOPHOREA of clevelandellids have conspicuous polysaccha- ride “skeletal” elements in their cortex, an “armor” of a different sort (see Albaret, 1970a). Like the Class SPIROTRICHEA , there is no conspicuous synapomorphy for members of this class. They are united by the following three fea- tures. First, they are restricted to anaerobic habitats and are typically dependent upon methanogenic symbionts . Although this is not a unique feature for the Class ARMOPHOREA (see particularly Chapter 12. Class PLAGIOPYLEA ), we predict that the metabolic dependence on hydrogenases in this class will be shown to have a common phylogenetic origin. Second, clevelandellids and armophorids share pleurotelokinetal stomatogen- esis of the adoral polykinetids , a feature shown by members of other classes (Foissner & Agatha, 1999). Finally, they show strong similarities in the sequences of their small subunit rRNA (SSUrRNA) genes (Embley et al., 1995; Hackstein, Van Hoek, Leunissen, & Huynen, 2001; van Hoek, van Alen, Sprakel, Hackstein, & Vogels, 1998). This class could be called the first “ riboclass ” of ciliates, since its monophyly is predicted by sequence analyses of the SSUrRNA genes. However, we do not yet have a signature sequence that would char- acterize the class. 8.1 Taxonomic Structure The two major groups – the clevelandellids and armophorids – included in this class have long been considered heterotrichs because of their pos- session of multiple adoral polykinetids (Fig. 8.1). Corliss (1979) considered them to be suborders within the Order Heterotrichida . However, early ultrastructural analysis demonstrated clear differ- ences between the somatic and oral structures of clevelandellids and their presumed “ heterotrich ” relatives. The somatic dikinetids do not give rise to postciliodesmata , their kinetodesmal fibril is differ- ently shaped, and there is a prominent left-directed striated cathetodesmal fibril arising adjacent to the anterior kinetosome (Paulin, 1967; de Puytorac & Grain, 1969, 1976). Although there is still no pub- lished account devoted solely to the ultrastructure of armophorids , Schrenk and Bardele (1991) have indicated differences between the somatic kinetid of the armophorid Metopus and those of cleve- landellids . It does appear that Metopus may have cathetodesmal-like fibrils , which do not appear striated. Little research has been done on members of this class, outside the recent interest in their symbiotic methanogens (see below Life History and Ecology ). We place armophorids and clevelandellids in the Class ARMOPHOREA primarily based on their strong association derived from sequence simi- larities of the SSUrRNA gene: the clevelandellids Nyctotherus and Nyctotheroides strongly group with the armophorids Metopus and Caenomorpha (Embley et al., 1995; van Hoek et al., 1998). Both Jankowski (1968b) and Albaret (1975) have sug- gested that clevelandellids may have derived from metopids through transformation of the cortical patterning, following a suggestion by Villeneuve- Brachon (1940). Therefore, we place these two groups together and elevate them to ordinal status, as others have done (Lynn & Small, 1997, 2002; de Puytorac, 1994a; Small & Lynn, 1985). Following Jankowski (1964a, 1964b, 1968b) and Albaret (1975), we assume that the free-living armophorids represent the descendants of the ancestral group from which the endosymbiotic cleve- landellids evolved. The Order Armophorida includes two fami- lies: the Family Metopidae and the Family Caenomorphidae (Fig. 8.1). In most forms, there is a slight twist left to the anterior end of the body, which is covered by up to five perizonal or epistomial kineties (e.g., Fernández-Galiano & Fernández-Leborans, 1980; Jankowski, 1968b). This twist becomes pronounced in derived forms and in all caenomorphids (Fig. 8.1). Caenomorphids are not typically holotrichous, but rather may have the somatic ciliation restricted to anterior and pos- terior cirrus-like tufts. The Order Clevelandellida has not changed in composition since Corliss (1979). It contains five families: the Family Nyctotheridae , the Family Sicuophoridae , the Family Clevelandellidae , the Family Inferostomatidae , and the Family Nathellidae . The latter two families are mono- typic. Clevelandellids are densely ciliated, often laterally compressed ciliates with many