Trichite features contribute to the revision of the genus Strombidium (Alveolata, Ciliophora, Spirotricha).

Strombidium is a species-rich genus of oligotrichid ciliates mainly inhabiting the marine pelagial. In molecular phylogenies, the genus emerged as non-monophyletic, and cladistic analyses suggest that it is largely characterized by plesiomorphies. A reliable split of the genus and the establishment of new genera necessitate, however, support by novel morphological and/or ultrastructural features. In the present study, the arrangement and ultrastructure of trichites are proposed as taxonomically relevant characters. Strombidium biarmatum Agatha et al., 2005 differs in the trichite pattern from the type species Strombidium sulcatum and most congeners. Aside from the trichites inserting anteriorly to the girdle kinety and generating the typical funnel-shaped complex in the posterior cell portion, the species displays additional trichites between the adoral membranelles even visible in live cells. Here, this exceptional trichite arrangement is detailed based on transmission electron microscopic investigations. In molecular phylogenies, S. biarmatum forms a monophylum with two congeners sharing its trichite arrangement. Therefore, the strombidiid genus Heteropilum nov. gen. is established with S. biarmatum as type species to also include H. paracapitatum (Song et al., 2015) nov. comb. and H. basimorphum (Martin & Montagnes, 1993) nov. comb. Further differences discovered in the trichite ultrastructure support the organelles' taxonomic significance.

A comparative ultrastructural study on the nanoscale extrusomes of tintinnids (Alveolata, Ciliophora, Spirotricha) and their phylogenetic significance.

The capsules, putative extrusomes in tintinnid ciliates, are known since 1971. Based on their ultrastructure, shape, and size, five capsule types were distinguished and suggested to be of phylogenetic significance. However, detailed morphometric data and transmission electron micrographs are lacking to verify former conclusions. In the current study, comprehensive analyses of transmission electron microscopic data were performed, investigating 14 species from 13 genera and more than seven families collected in European coastal waters and in the Northeast Pacific. Our data suggest two main capsule types (large and ampulliform vs small and ellipsoidal/ovoidal) each including two subtypes characterised by their internal structures. Species groupings inferred from the capsule (sub-)types emerge also as closely related in gene trees. Additionally, the ampulliform type unites the Undellidae, Xystonellidae, and Tintinnid clade 2, while the shared possession of the small ellipsoidal type proposes a close relationship of Tintinnid clade 11 with the Rhabdonellidae and Cyttarocylididae. Thus, the capsules provide promising features to shed light on several unresolved evolutionary relationships among tintinnid genera and families; yet, information on capsules is still missing for many monophyletic groupings. Finally, we provide the first ultrastructural clues for the extrusive character of these organelles.

A light and electron microscopical study on the resting cyst of the tintinnid Schmidingerella (Alveolata, Ciliophora) including a phylogeny-aware comparison.

Resting cysts protect ciliates against adverse environmental conditions. The morphology and ultrastructure of resting cysts has been described in very few Oligotrichea, a group of mainly marine planktonic ciliates. The present study provides the first ultrastructural data for loricate choreotrichids, applying light and electron microscopy on the cysts of the tintinnid Schmidingerella meunieri (Kofoid and Campbell, 1929) Agatha and Strüder-Kypke, 2012. The morphology of live cysts and the wall ultrastructure of cryofixed cysts were morphometrically analysed. The resting cyst is roughly flask-shaped, broadening to a slightly concave, laterally protruding anterior plate. An emergence pore closed by a skull cap-shaped papula is directed to the bottom of the lorica on the opposite side of the cyst. The cyst wall consists of an ectocyst, mesocyst, and endocyst differing in thickness, structure, and nitrogen concentration as revealed by conventional transmission electron microscopy, electron energy loss spectroscopy, and electron spectroscopic imaging. The cysts of S. meunieri belong to the kinetosome-resorbing type, which also occurs in the majority of hypotrich ciliates. Two main features (flask-shape and presence of an emergence pore) are shared with the closely related aloricate choreotrichids and oligotrichids, distinguishing the Oligotrichea from the hypotrich and the more distantly related euplotid ciliates.

Molecular signature characters complement taxonomic diagnoses: A bioinformatic approach exemplified by ciliated protists (Ciliophora, Oligotrichea).

Traditionally, taxa following the botanical or zoological codes of nomenclature are diagnosed mainly by morphological characters, although integrative taxonomy advocates including additional features. While many taxonomic studies include DNA sequence analyses, a systematic integration of diagnostic molecular characters (signature characters) is still rare. Here, we suggest a practical guideline for the detection and evaluation of signature characters that provides the means necessary to complement diagnoses and facilitates identifications. The guideline comprises generally applicable criteria exemplified by a case study on an ecologically important group of planktonic protists, the Oligotrichea. The detection of signature characters and their discrete states in multiple sequence alignments is facilitated by the recently developed tool DeSignate. Moreover, we introduce a novel bioinformatic approach to test the influence of different alignment programs on the consistency of signature characters. Our workflow enabled detection of consensus signature characters for most tested taxa and inclusion of such characters in the diagnoses of three orders, eight families, and two genera in the Oligotrichea. The suggested approach is a step towards an integrative taxonomy linking reliable molecular sequence data to organisms' traits.

The importance of type species and their correct identification: A key example from tintinnid ciliates (Alveolata, Ciliophora, Spirotricha).

Types and the corresponding rules in the International Code of Zoological Nomenclature are crucial for taxonomy and are meant to provide nomenclatural stability. In the case of neotypification, especially diligent taxonomic work is required to retain continuity. In the present communication, we first outline the main principles of typification and neotypification. We then discuss a critical case, using a current example from the marine planktonic tintinnid genus Tintinnopsis Stein, 1867 (Alveolata, Ciliophora). This diverse and ubiquitous genus is nonmonophyletic, but its revision and the erection of new related genera is currently prevented by the uncertain affiliation of its type species.

DeSignate: detecting signature characters in gene sequence alignments for taxon diagnoses.

BACKGROUND: Molecular characters have been added in integrative taxonomic approaches in recent years. Nevertheless, taxon diagnoses are still widely restricted to morphological characters. The inclusion of molecular characters into taxon diagnoses is not only hampered by problems, such as their definition and the designation of their positions in a reference alignment, but also by the technical effort. RESULTS: DeSignate is a tool for character-based taxon diagnoses that includes a novel ranking scheme. It detects and classifies individual and combined signature characters (diagnostic molecular characters) based on so-called character state vectors. An intuitive web application guides the user through the analysis process and provides the results at a glance. Further, formal definitions and a uniform terminology of characters are introduced. CONCLUSIONS: DeSignate facilitates the inclusion of diagnostic molecular characters and their positions to complement taxon diagnoses. Compared to previous solutions, the tool simplifies the workflow and improves reproducibility and traceability of the results. The tool is freely available as a web application at (https://designate.dbresearch.uni-salzburg.at/) and is open source (https://github.com/DatabaseGroup/DeSignate/).

Redescription of Antetintinnidium mucicola (Claparède and Lachmann, 1858) nov. gen., nov. comb. (Alveolata, Ciliophora, Tintinnina).

Tintinnid ciliates have traditionally been described and classified exclusively based on their lorica features. Although information on the cell characters is urgently needed for a natural classification, more molecular than cytological data has been accumulated over recent years. Apparently, the tintinnids developed in the marine environment and entered freshwater several times independently. Typical freshwater tintinnids belong to the genera Tintinnidium and Membranicola. The species are comparatively well-known regarding their morphology and characterised by two unusual de novo originating ciliary rows, the ventral organelles. In contrast, the cell features in the marine/brackish Tintinnidium species, specifically their somatic ciliary patterns, are insufficiently known or not known at all. Therefore, the morphology of a common marine/brackish representative, Tintinnidium mucicola, is redescribed based on live observation and protargol-stained material. Furthermore, biogeographical and autecological data of the species are compiled from literature and own records. The phylogenetic relationships of T. mucicola are inferred and the diversity of the family Tintinnidiidae is assessed from 18S rDNA sequences. The study shows that T. mucicola is not only molecularly distinct, but also characterised by many plesiomorphic features, for instance, it does not possess a verifiable homologue to the ventral organelles. Hence, a new genus, Antetintinnidium nov. gen., is established for T. mucicola. The new insights into the diversity of Tintinnidiidae shed light on the early evolution of tintinnids and might provide clues on their adaptions to freshwater.