Electron microscopical observations on the ciliate Furgasonia blochmanni Fauré-Fremiet, 1967: Part I: An update on morphology

Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within "Nassophorea-Synhymenia-Phyllopharyngea" Assemblage

Ciliated protists (ciliates) are widely used for investigating evolution, mostly due to their successful radiation after their early evolutionary branching. In this study, we employed high-throughput sequencing technology to reveal the phylogenetic position of Synhymenia, as well as two classes Nassophorea and Phyllopharyngea, which have been a long-standing puzzle in the field of ciliate systematics and evolution. We obtained genomic and transcriptomic data from single cells of one synhymenian (Chilodontopsis depressa) and six other species of phyllopharyngeans (Chilodochona sp., Dysteria derouxi, Hartmannula sinica, Trithigmostoma cucullulus, Trochilia petrani, and Trochilia sp.). Phylogenomic analysis based on 157 orthologous genes comprising 173,835 amino acid residues revealed the affiliation of C. depressa within the class Phyllopharyngea, and the monophyly of Nassophorea, which strongly support the assignment of Synhymenia as a subclass within the class Phyllopharyngea. Comparative genomic analyses further revealed that C. depressa shares more orthologous genes with the class Nassophorea than with Phyllopharyngea, and the stop codon usage in C. depressa resembles that of Phyllopharyngea. Functional enrichment analysis demonstrated that biological pathways in C. depressa are more similar to Phyllopharyngea than Nassophorea. These results suggest that genomic and transcriptomic data can be used to provide insights into the evolutionary relationships within the "Nassophorea-Synhymenia-Phyllopharyngea" assemblage.

Ultrastructural Studies on a Model Tintinnid - Schmidingerella meunieri (Kofoid and Campbell, 1929) Agatha and Strüder-Kypke, 2012 (Ciliophora). I. Somatic Kinetids with Unique Ultrastructure

Molecular phylogenies of Oligotrichea currently do not contain all genera and families and display topologies which are often incongruent with morphological findings. In ciliates, the somatic kinetids are rather conserved, i.e., their ultrastructures, particularly the fibrillar associates, often characterise the main groups, except for the choreotrichids. Four different kinetid types are found in protargol-stained choreotrichids and used for reconstructing the taxon's evolution (the "Kinetid Transformation Hypothesis"). Proof for this hypothesis requires transmission electron microscopic studies, which are very rare in the choreotrichids and oligotrichids. Such an approach provides insights into the ultrastructural variability of somatic kinetids in spirotrichs and may also detect apomorphies characterising certain choreotrichid families. In the model tintinnid Schmidingerella meunieri, the ultrastructure of the three kinetid types in the somatic ciliature is studied in cryofixed cells. The data support the "Kinetid Transformation Hypothesis" regarding tintinnids with a ventral kinety. This first detailed study on kinetids in tintinnids and choreotrichids in general reveals totally new kinetid types in ciliates: beyond the three common associates, they are characterised by two or three conspicuous microtubular ribbons extending on the kinetids' left sides. These extraordinary ribbons form together with the overlapping postciliary ribbons a unique network in the cortex of the anterior cell portion. The evolutionary constrains which might have fostered the development of such structures are discussed for the Oligotrichea, the choreotrichids, and tintinnids as their first occurrence is currently uncertain. Additionally, the kinetids in tintinnids, aloricate choreotrichids, oligotrichids, hypotrichs, and euplotids are compared.

Electron microscopical observations on the ciliate Furgasonia blochmanni Fauré-Fremiet, 1967: Part II: Morphogenesis and phylogenetic conclusions

The ultrastructural events during cortical morphogenesis of Furgasonia blochmanni are studied by TEM. The kinetosomal proliferation in the somatic cortex at the beginning of morphogenesis produces kinetosomal triads. All kinetosomes of these triads have the same fibrillar systems as somatic monokinetids. Such somatic triads are also involved in the formation of the adoral membranelies of the opisthe. In the mature adoral membranelies the postciliary microtubules of the anterior and the middle kinetosomes of these triads as well as all kinetodesmal fibers are replaced by desmoses. Only the opisthe gets new adoral membranelles, since the parental adoral membranelles persist in the proter; however, the new paroral membrane of both the proter and the opisthe are newly formed as derivatives of the old paroral membrane. At the beginning of stomatogenesis the old paroral membrane divides into 2 parts of unequal length. The anterior part, which stays in the proter, splits longitudinally forming a new kinety 1' and the anlage of the new paroral membrane. In the adult cell the anterior kinetosomes of the paroral dyads (the right kinetosomes of the paroral membrane) are already orientated like somatic kinetosomes. Therefore, no rotation is necessary when these kinetosomes become part of the somatic monokinetids of kinety 1'. The posterior kinetosomes of the dyads of the anterior part of the paroral membrane (the anlage of a new paroral membrane of the proter) remain orientated perpendicularly to the longitudinal axis of the cell, an orientation which is necessary when these kinetosomes send postciliary microtubules towards the forming cytopharyngeal basket. All kinetosomes of the posterior part of the former paroral membrane also become orientated such that triplet 9 points to the left towards the presumptive oral opening of the opisthe. During stomatogenesis both kinetosomes of the new paroral membranes are rotated by 90° compared to the longitudinal axis of the cell and send postciliary microtubules towards the forming cytopharynx. In contrast to the adult cell, during stomatogenesis only the posterior kinetosomes of the paroral dyads are ciliated while the newly formed anterior kinetosomes are barren. At the end of stomatogenesis the cilia of the posterior kinetosomes are resorbed and new cilia grow at the anterior kinetosomes. During stomatogenesis all kinetosomes of the anlagen of the new paroral membranes possess postciliary microtubules, kinetodesmal fibers and in some cases transverse microtubules as well. Following stomatogenesis, the kinetodesmal fibers and transverse microtubules are resorbed, and the orientation of the anterior kinetosomes reverts from perpendicular to parallel to the paroral membrane axis. These data from F. blochmanni are compared with the ultrastructural data on morphogenesis from Paraurostyla, Tetrahymena and Coleps. Finally the phylogenetically significant characters obtained from studies on morphology and morphogenesis in F. blochmanni and other nassulid ciliates are discussed, and a "scheme of argumentation of phylogenetic systematics" is presented for the nassulids. It is concluded that F. blochmanni is correctly classified within the nassulid suborder Nassulina and that the Nassulida including F. blochmanni certainly are a monophyletic group within the subphylum Cyrtophora Small, 1976.

Phylogeny and systematic position of Zosterodasys (Ciliophora, Synhymeniida): a combined analysis of ciliate relationships using morphological and molecular data

The Synhymeniida is characterized both by a band of somatic dikinetids, the synhymenium, extending across the surface of the cell and by a ventral cell mouth lacking specialized feeding cilia but subtended by a well-developed cyrtos. The synhymeniids have been hypothesized to be members of the class Nassophorea but our previous ultrastructural study of the synhymeniid genus Zosterodasys did not show any clear synapomorphies that would permit definitive placement in the Nassophorea or as a sister taxon to any of the other ciliate groups possessing a cyrtos. In the present study, simultaneous analysis of morphological and small subunit rDNA molecular data indicates that the Synhymeniida are sister to the class Phyllopharyngea and that this clade is, in turn, sister to the remaining Nassophorea, although this result is sensitive to dataset inclusion and alignment parameters. While this suggests that taxa with a ventral cyrtos might be united into a named taxon (e.g. resurrecting the Hypostomata), additional data are needed to reach a definitive conclusion.

Small subunit rRNA phylogenies show that the class nassophorea is not monophyletic (Phylum Ciliophora)

The hypostome ciliates have been generally classified into two classes, Phyllopharyngea and Nassophorea. The status of Nassophorea and its relationship with Phyllopharyngea is one of the most controversial issues in ciliate systematics. Here we focus on the phylogenetic interrelationships of Nassophorea and Phyllopharyngea based on small subunit ribosomal RNA gene sequences. The three nassophorean subgroups, synhymeniids, microthoracids, and nassulids, each emerged as monophyletic, with synhymeniids as a sister group of Phyllopharyngea, and microthoracids as a sister of the synhymeniids+Phyllopharyngea clade in all phylogenies. The exact placement of the nassulids, however, remains uncertain. Following a detailed analysis of phenotypic characters, we hypothesize that: (1) the Phyllopharyngea could have evolved from synhymeniids, with the further development of their subkinetal microtubules as one of the major events; and (2) the development of monokinetid structures, as well as the reduction and specialization of the cyrtos and cortex, might have occurred during the diversifications of the microthoracids, synhymeniids, and Phyllopharyngea from a common ancestor. Expanding the class Phyllopharyngea to include the synhymeniids as a subclass, and designating a new subclass Subkinetalia n. subcl. for the group comprising cyrtophorians, chonotrichians, rhynchodians, and suctorians, are proposed.

Centrin-like filaments in the cytopharyngeal apparatus of the ciliates Nassula and Furgasonia: evidence for a relationship with microtubular structures

The cytopharyngeal apparatus in the Nassulinid ciliates Nassula and Furgasonia is a highly specialized microtubular/filamentous organelle designed for ingestion of organisms such as filamentous bacteria. From studies on living cells, it was previously shown that this organelle, also called "feeding basket," guides the filamentous bacteria and manipulates them to some extent during the early steps of ingestion. This results in a complex sequence of movements where the basket is successively dilated and constricted in its upper part. Whereas some of these movements (dilation) seem to be intrinsic to the microtubular components of the basket, others (constriction) are believed to be mediated by contractile filamentous structures [Tucker, 1968: J. Cell Sci. 3:493-514]. In this study, we have used antibodies raised against ciliate centrins to demonstrate these proteins by Western blot and immunocytochemical methods in Nassula and Furgasonia. In both ciliates, a 20-kDa centrin immunoanalog was localized in the upper (contractile) part of the cytopharyngeal apparatus. Immunoelectron microscopy revealed that cytopharyngeal centrin is engaged in filamentous material, forming a sphincter-like structure possibly involved in the movements of contraction. Interestingly, physical links were noted between filaments labeled for centrin and cytopharyngeal microtubules. The mechanistic implications of these findings are discussed.

Phylogenetic relationships of the Nassulida within the phylum Ciliophora inferred from the complete small subunit rRNA gene sequences of Furgasonia blochmanni, Obertrumia georgiana, and Pseudomicrothorax dubius

Using comparisons of complete small subunit rRNA sequences from the ciliated protozoans Furgasonia blochmanni, Obertrumia georgiana, and Pseudomicrothorax dubius we inferred the phylogenetic position of the Nassulida (Class Nassophorea) within the Ciliophora. In distance matrix analyses the Nassulida share a common ancestry with the colpodean ciliate Colpoda inflata. Distance matrix and parsimony methods convincingly demonstrate that the Nassulida plus Colpodida are members of a complex ciliate assemblage that also includes the oligohymenophorans and phyllopharyngeans. These phylogenetic inferences are largely congruent with recent analyses of 23S-like rRNA gene sequences and morphogenetic features. Groups traditionally thought to represent ancestral lineages now appear as highly derived ciliates. In contrast, heterotrichs which were considered to represent a highly evolved group, diverge at the base of the ciliates.

Somatic kinetics or paroral membrane: which came first in ciliate evolution?

The ciliate species which lack a distinctive oral ciliature are considered to represent an ancestral state in ciliate evolution. Consequently, the somatic kineties composed of kinetids (kinetosomes plus cilia and associated fibrillar systems) are thought to be the ancestral ciliature. Results on stomatogenesis in 'gymnostomial ciliates' have shown that these ciliates probably have evolved from ancestors already equipped with an oral ciliature. Thus instead of the somatic, the oral ciliature may be regarded an ancestral. Based on these ideas a hypothesis on the evolution of the ciliate kinetome (assembly of all kinetids covering the body of a given ciliate) is presented. The first step in the evolution of the kinetome was the formation of a paroral membrane, a compound ciliary organelle lying along the right side of the oral area which historically but falsely is termed membrane. It was composed of kinetosomal dyads (dikinetids), derived from the kinetid of a dinoflagellate-like ancestor. From the beginning the paroral membrane was responsible for locomotion, ingestion and for the formation of a cytopharyngeal tube which the first ciliate probably had inherited from its flagellate ancestor. In the second step a first somatic kinety was formed from the right row of kinetosomes of the paroral membrane as a result of a longitudinal splitting of the paroral membrane and a subsequent migration of the forming kinety to the right into the somatic cortex. To increase the number of somatic kineties this process was repeated until the kinety produced first reached the left border of the oral area. By this step the locomotive and the nutritional functions were differentiated between somatic and oral structures. In a third step the adoral organelles were formed from somatic kinetids left of the oral area. The primitive type of stomatogenesis was a buccokinetal one derived from the mode the flagellate ancestor used to distribute its replicated kinetosomes to the offspring cells (buccokinetal means that at least parts of the oral anlage for the posterior offspring cell has its origin in the parental oral apparatus). This hypothesis, based on comparative studies on ciliate morphogenesis, is corroborated by molecular data from other laboratories.

Phylogenetic relationships within the class Oligohymenophorea, phylum Ciliophora, inferred from the complete small subunit rRNA gene sequences of Colpidium campylum, Glaucoma chattoni, and Opisthonecta henneguyi

Phylogenetic relationships within the class Oligohymenophorea, phylum Ciliophora, were investigated by determining the complete small subunit rRNA (SSrRNA) gene sequences for the hymenostomes Colpidium campylum, Glaucoma chattoni, and the peritrich Opisthonecta henneguyi. The affiliations of the oligohymenophoreans were assessed using both distance matrix (DM) and maximum parsimony (MP) analyses. Variations do exist in the phylogenies created by the two methods. However, the basic tree topologies are consistent. In both the DM and MP analyses the hymenostomes (C. campylum, G. chattoni, and the tetrahymenas) all form a very tight group associated with the peritrich O. henneguyi. The Tetrahymena lineage was monophyletic whereas Colpidium and Glaucoma were more closely related to each other than either was to the tetrahymenas. The monophyly of the genus Tetrahymena in the present analysis supports the phylogenies determined from morphological data and molecular sequence data from the histone H3II/H4II region of the genome. The perplexing and controversial phylogenetic position of the peritrichs is once again depicted in the present analysis. The distinctiveness of the peritrich Opisthonecta from both hymenostome and nassophorean ciliates based on evolutionary distances suggests that the elevation of the peritrichs to a higher taxonomic rank should be reconsidered.