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 Abstract The ciliated protozoa are a distinct group of 
protists characterized by (1) the presence of cilia de-
rived from kinetosomes with three fi brillar associates; 
(2) nuclear dimorphism; and (3) conjugation as a 
sexual process. They are exceedingly diverse in 
shape and size, and may have evolved over 2 billion 
years ago. The ciliate body form likely evolved from 
a fl agellate that proliferated kinetids near its oral 
apparatus, and these kinetids became fi rst the ciliate 
paroral, which itself replicated to provide somatic 
kineties and fi nally the adoral kinetids. Ciliates are 
now divided into two subphyla and 11 classes based 
on features of nuclear division and the pattern of 
fi brillar associates in their somatic kinetids. They 
are found in a diversity of microhabitats, with the 
majority of species likely cosmopolitan. However, 
endemism appears to be characteristic of perhaps as 
many as 30% of the species. Ciliates are important 
components of the microbial loop, often responsible 
for consuming the majority of primary production 
and bacterial production in certain habitats. 
 Their development is complex since the kinetid 
patterns of the somatic and oral cortex are them-
selves complex. This complexity has made them 
useful models for developmental biologists while 
the systematists have used these patterns to relate 
different taxa to each other. The life cycles of cili-
ates are also complex and clearly separate sexual 
processes from asexual reproduction. Sexual proc-
ess, conjugation, occurs in the context of a breeding
strategy, ranging from an inbreeding one to an 
outbreeding one. A new macronucleus typically 
develops at each conjugation cycle through a com-
plicated set of processes of DNA fragmentation, 
diminution, and replication. However, this process 
likely occurs at each cell cycle in karyorelictean 
ciliates whose macronuclei do not divide. 
 Keywords Cytotaxis, structural guidance, extru-
some, metachrony, alveoli 
 The ciliates, without doubt, are a most homo-
geneous group, which have long been separated 
from other protists. They are briefly distinguished 
by three major features: (1) by their cilia, variable 
in number and arrangement, distributed over the 
body surface and derived from kinetosomes with 
three typical fibrillar associates – the kinetodesmal 
fibril , the postciliary microtubular ribbon , and the 
 transverse microtubular ribbon ; (2) by their two 
kinds of nuclei – a macronucleus and a micro-
nucleus , the former controlling the physiological 
and biochemical functions of the cell and the latter 
as a germ-line reserve; and (3) by conjugation , 
a sexual process in which partners typically fuse 
temporarily to exchange gametic nuclei. All cili-
ates are heterotrophic and most possess a mouth, 
although some are mouthless (e.g., the astomes ) 
and others could be called polystomic (e.g., sucto-
rians with their tentacles). 
 Ciliates vary in shape and size. There are 
stalked and colonial species that have unusual 
forms, but generally the shapes are simple geo-
metric ones – spheres, cones, oblate spheroids, 
and cylinders, which may be flattened dorsoven-
trally in substrate-oriented species. Body form is 
relatively permanent since the cortex is supported 
by a complex microtubular and microfilamentous 
cytoskeleton. Ciliates range in size from 10 µm in 
very small spheroid forms to 4,500 µm in highly 
 Chapter 4 
 Phylum CILIOPHORA – Conjugating, 
Ciliated Protists with Nuclear Dualism 
90 4. Phylum CILIOPHORA – Conjugating, Ciliated Protists with Nuclear Dualism
elongate and contractile ones. Biovolume ranges 
give another impression of size: in the Class 
 COLPODEA , cell volume ranges from 10 2 µm 3 for 
Nivaliella to 10 8 µm 3 for Bursaria ; and in the Class 
 OLIGOHYMENOPHOREA , cell volumes range 
from 10 3 µm 3 for some Cyclidium species to >10 9
µm3 for the trophonts of Ichthyophthirius (Lynn & 
Corliss, 1991). 
 Ciliates were first observed microscopically 
by van Leeuwenhoek (1674), the founder of pro-
tozoology (Corliss, 1975b). Ciliates were visible 
as blooms or colored waters in both marine and 
freshwater habitats, probably thousands of years 
before van Leeuwenhoek’s discoveries. Their for-
mal nomenclatural history begins in 1767 with the 
establishment of Vorticella by Linnaeus (Aescht, 
2001). They were named the INFUSORIA through-
out the 19th century, a name that was replaced in 
the early 20th century by the present name of the 
phylum – CILIOPHORA . The ciliates were an 
isolated group until 1991 when it was proposed 
that the membrane-bound sacs underlying their 
plasma membrane, the alveoli , were a synapo-
morphy or shared-derived character for a major 
clade of protists, the ALVEOLATA , which initially 
included dinoflagellates , apicomplexans , and cili-
ates (Cavalier-Smith, 1991; Wolters, 1991). This 
clade was reaffirmed in the revised classification of 
the protists proposed by Adl et al. (2005). Based on 
strong molecular evidence, this clade now includes 
these three major groups, along with the aber-
rant “ dinoflagellate ” Oxyrrhis and the perkinsids 
associated with the dinoflagellate clade and several 
flagellates, such as Colpodella , associated with the 
base of the apicomplexan clade. Dinoflagellates 
and apicomplexans are strongly supported as sister 
taxa, leaving the ciliates as a separate lineage 
(Leander & Keeling, 2003). When and how the cil-
iates diverged from the alveolate common ancestor 
are still open questions, but we have some ideas. 
 With regard to when, ciliates probably arose 
in the Precambrian era . While there are no fos-
sils from this time, Wright and Lynn (1997c) 
argued that the phylum could be over 2 billion 
years old, based on the rate of evolution of the 
small subunit rRNA molecular clock (Fig. 4.1). 
While this estimate can be challenged as it makes 
some strong assumptions on the constancy of the 
 molecular clock , there is no dispute over fossils 
of the loricate tintinnines , which stretch from the 
 Ordovician period of the Paleozoic era , some 400–450 
million years before present (myBP) into the 
 Pleistocene , about 1 myBP. Tintinnine fossils are 
most abundant in the sediments of the Jurassic and 
 Cretaceous periods of the Mesozoic era (see Bonet, 
1956; Colom, 1965; Tappan & Loeblich, 1968, 
1973). Fossils of other loricate forms have also 
been found: Deflandre and Deunff (1957) reported 
a fossil folliculinid heterotrich while Weitschat 
and Guhl (1994) described several fossil loricate 
peritrichs from the Lower Triassic period . Even 
more recently, extremely well-preserved ciliates, a 
Paramecium species and several colpodeans, have 
been described from amber derived from southern 
Germany in amber-bearing sandstone deposits 
(Schönborn, Dörfelt, Foissner, Krientiz, & Schäfer, 
1999), which have now been assigned to the Late 
Cretaceous , some 90 million years ago (Schmidt, 
von Eynatten, & Wagreich, 2001). However, these 
fossil forms can generally be placed in contempo-
rary families and even genera, so they provide little 
insight into the origin of the ciliates. Nevertheless, 
this has not deterred some speculation on how 
ciliates diverged. Given the molecular phylogenies, 
there is no doubt that the ciliates evolved from a 
flagellate ancestor. Two major features of ciliates 
– their complex cortex and their nuclear dualism 
– have preoccupied those who have speculated on 
how a flagellate ancestor might have evolved into 
the ancestral ciliate. 
 The complex ciliate cortex undoubtedly evolved 
from a simpler flagellate dikinetid. Earlier evolu-
tionary schemes of Orias (1976) and Small (1984) 
argued that the dikinetids of the flagellate ances-
tor replicated to form first a “torsionless chain”, 
similar to the polynergid dinoflagellate Polykrikos , 
and then a ribbon-like form with multiple somatic 
kineties . Orias imagined that the ribbon-like