Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis

Liu, Mingjian, Li, Lifang, Qu, Zhishuai, Luo, Xiaotian, Al-Farraj, Saleh A., Lin, Xiaofeng, Hu, Xiaozhong (2017): Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis. Acta Protozoologica 56 (1): 17-37, DOI: 10.4467/16890027AP.17.003.6967, URL: https://www.mendeley.com/catalogue/cb3bc4f7-739f-32f8-92cd-7da31a838cb6

Redescription of Dexiotricha colpidiopsis (Kahl, 1926) Jankowski, 1964 (Ciliophora, Oligohymenophorea) from a Hot Spring in Iceland with Identification Key for Dexiotricha species

Publisher's version (útgefin grein)We isolated an encysted ciliate from a geothermal field in Iceland. The morphological features of this isolate fit the descriptions of Dexiotricha colpidiopsis (Kahl, 1926) Jankowski, 1964 very well. These comprise body shape and size in vivo, the number of somatic kineties, and the positions of macronucleus and contractile vacuole. Using state-of-the-art taxonomic methods, the species is redescribed, including phylogenetic analyses of the small subunit ribosomal RNA (SSU rRNA) gene as molecular marker. In the phylogenetic analyses, D. colpidiopsis clusters with the three available SSU rRNA gene sequences of congeners, suggesting a monophyly of the genus Dexiotricha. Its closest relative in phylogenetic analyses is D. elliptica, which also shows a high morphological similarity. This is the first record of a Dexiotricha species from a hot spring, indicating a wide temperature tolerance of this species at least in the encysted state. The new findings on D. colpidiopsis are included in a briefly revision of the scuticociliate genus Dexiotricha and an identification key to the species.This study was funded by grants awarded to TS by Europlanet 2020 (project 15-EPN-006) and by the Bundesministerium für Bildung und Forschung (BMBF)/Deutsches Zentrum für Luft- und Raumfahrt (DLR, grant 50WB1737). Europlanet 2020 RI has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 654208. Zhishuai Qu received funds from the China Scholarship Council (CSC). We thank Fengchao Li for his support with species identification and Natasa Desnica (Matis) for the trace metal analysis.Peer Reviewe

Two parasitic ciliates (Protozoa: Ciliophora: Phyllopharyngea) isolated from respiratory-mucus of an unhealthy beluga whale: characterization, phylogeny and an assessment of morphological adaptations

Abstract Ciliates occur in the blowholes of marine mammals, but our understanding of their biology is poor. Consequently, we investigated an infestation of ciliates in an unhealthy, captive beluga whale that was exhibiting accelerated breathing, leukocytosis and expulsion of unusually large amounts of viscous sputum. This sputum contained ~104 ciliates mL-1 (when healthy, numbers were ten- to 100-fold lower). One known ciliate species, Planilamina ovata, is fully characterized, and a new species, Kyaroikeus paracetarius sp. nov., is here described. The new species is established based on its larger number of left kineties over its only congener. Sequences of small-subunit rDNA, large-subunit rDNA and ITS1-5.8S-ITS2 regions of these two taxa were used in phylogenetic analyses, inferring that Kyaroikeus and Planilamina have close affinity with the free-living family Dysteriidae, contradicting their morphology-based assignment to the family Kyaroikeidae. We suggest that Kyaroikeidae be relegated to subfamily status. Finally, by comparing parasitic species with free-living taxa, we suggest how these ciliates have adapted to their unique environment and how they may have initially invaded the host. We provide essential data and concepts for the continued evaluation of ciliate-parasites in whale blowholes.</jats:p

Seasonality of Planktonic Freshwater Ciliates: Are Analyses Based on V9 Regions of the 18S rRNA Gene Correlated With Morphospecies Counts?

Ciliates represent central nodes in freshwater planktonic food webs, and many species show pronounced seasonality, with short-lived maxima of a few dominant taxa while many being rare or ephemeral. These observations are primarily based on morphospecies counting methods, which, however, have limitations concerning the amount and volume of samples that can be processed. For high sampling frequencies at large scales, high throughput sequencing (HTS) of freshwater ciliates seems to be a promising tool. However, several studies reported large discrepancy between species abundance determinations by molecular compared to morphological means. Therefore, we compared ciliate DNA metabarcodes (V9 regions of the 18S rRNA gene) with morphospecies counts for a 3-year study (Lake Zurich, Switzerland; biweekly sampling, n = 74). In addition, we isolated, cultivated and sequenced the 18S rRNA gene of twelve selected ciliate species that served as seeds for HTS analyses. This workflow allowed for a detailed comparison of V9 data with microscopic analyses by quantitative protargol staining (QPS). The dynamics of V9 read abundances over the seasonal cycle corroborated well with morphospecies population patterns. Annual successions of rare and ephemeral species were more adequately characterized by V9 reads than by QPS. However, numbers of species specific sequence reads only partly reflected rank orders seen by counts. In contrast, biomass-based assemblage compositions showed higher similarity to V9 read numbers, probably indicating a relation between cell sizes and numbers / sizes of macronuclei (or 18S rRNA operons). Full-length 18S rRNA sequences of ciliates assigned to certain morphospecies are urgently needed for barcoding approaches as planktonic taxa are still poorly represented in public databases and the interpretation of HTS data depends on profound reference sequences. Through linking operational taxonomic units (OTUs) with known morphospecies, we can use the deep knowledge about the autecology of these species

Morphology and SSU rDNA sequences of four cyrtophorian ciliates from China, with description of a new species (Protista, Ciliophora, Phyllopharyngea)

Wang, Congcong, Qu, Zhishuai, Hu, Xiaozhong (2019): Morphology and SSU rDNA sequences of four cyrtophorian ciliates from China, with description of a new species (Protista, Ciliophora, Phyllopharyngea). Zootaxa 4664 (2): 206-220, DOI: https://doi.org/10.11646/zootaxa.4664.2.

Lake ecosystem robustness and resilience inferred from a climate-stressed protistan plankton network

Network analyses of biological communities allow for identifying potential consequences of climate change on the resilience of ecosystems and their robustness to resist stressors. Using DNA metabarcoding datasets from a three-year-sampling (73 samples), we constructed the protistan plankton co-occurrence network of Lake Zurich, a model lake ecosystem subjected to climate change. Despite several documentations of dramatic lake warming in Lake Zurich, our study provides an unprecedented perspective by linking changes in biotic association patterns to climate stress. Water temperature belonged to the strongest environmental parameters splitting the data into two distinct seasonal networks (October–April; May–September). The expected ecological niche of phytoplankton, weakened through nutrient depletion because of permanent thermal stratification and through parasitic fungi, was occupied by the cyanobacterium Planktothrix rubescens and mixotrophic nanoflagellates. Instead of phytoplankton, bacteria and nanoflagellates were the main prey organisms associated with key predators (ciliates), which contrasts traditional views of biological associations in lake plankton. In a species extinction scenario, the warm season network emerged as more vulnerable than the cold season network, indicating a time-lagged effect of warmer winter temperatures on the communities. We conclude that climate stressors compromise lake ecosystem robustness and resilience through species replacement, richness differences, and succession as indicated by key network properties

Historical Review of Studies on Cyrtophorian Ciliates (Ciliophora, Cyrtophoria) from China

The subclass Cyrtophoria are a group of morphologically specialized ciliates which mainly inhabit soil, freshwater, brackish water, and marine environments. In this study, we revise more than 50 publications on the taxonomy, phylogeny, and ecology of cyrtophorian ciliates in China since the first publication in 1925, most of which were carried out in coastal areas. The research history can be divided into three periods: the early stage, the Tibet stage, and the molecular stage. To date, 103 morpho-species (147 isolates) have been formally recorded in China, with ciliature patterns described for 82 of them. A species checklist and an illustrated identification key to the genera are provided. A total of 100 small subunit rDNA sequences have been obtained for 74 taxonomic hits (lowest taxonomic rank to species or genus). These sequences are used for the study of molecular phylogeny. Based on these morphological data and molecular phylogeny analyses, we synthesize the understanding of the phylogeny of cyrtophorian ciliates. We hypothesize that the key evolutionary event of cyrtophorian ciliates lies in the separation of the stomatogenesis zone (postoral kineties) from the left kineties, namely, the formation of an independent &ldquo;sexual organelle&rdquo;. We, furthermore, briefly summarize the ecological features of cyrtophorian ciliates and provide a comprehensive bibliography of related research from China. Finally, we give an outlook on the future research directions of these taxa

A Case Study of the Morphological and Molecular Variation within a Ciliate Genus: Taxonomic Descriptions of Three Dysteria Species (Ciliophora, Cyrtophoria), with the Establishment of a New Species

Three Dysteria species, D. crassipes Claparede & Lachmann, 1859; D. brasiliensis Faria et al., 1922; and D. paracrassipes n. sp., were collected from subtropical coastal waters of the East China Sea, near Ningbo, China. The three species were studied based on their living morphology, infraciliature, and molecular data. The new species D. paracrassipes n. sp. is very similar to D. crassipes in most morphological features except the preoral kinety, which is double-rowed in the new species (vs. single-rowed in D. crassipes). The difference in the small ribosomal subunit sequences (SSU rDNA) between these two species is 56 bases, supporting the establishment of the new species. The Ningbo population of D. crassipes is highly similar in morphology to other known populations. Nevertheless, the SSU rDNA sequences of these populations are very different, indicating high genetic diversity and potentially cryptic species. Dysteria brasiliensis is cosmopolitan with many described populations worldwide and four deposited SSU rDNA sequences. The present work supplies morphological and molecular information from five subtropical populations of D. brasiliensis that bear identical molecular sequences but show significant morphological differences. The findings of this study provide an opportunity to improve understanding of the morphological and genetic diversity of ciliates

Uronema nigricans Florentin 1901

Uronema nigricans (Müller, 1786) Florentin, 1901 (Figs 2A, C, F, 3A–M, Table 1) Uronema nigricans has been redescribed several times since its first recording. However, high-quality photomicrographs of protargol-stained individuals and SSU rDNA sequencing were not available previously. In this study, we determined an improved diagnosis and a detailed redescription based on previous and present data. Improved diagnosis: Cell size ca. 20–50 μm × 10–25 μm in vivo with a truncated apical plate; pellicle thin and inconspicuously notched, with ridges located longitudinally along ciliary rows; 10–15 somatic kineties, somatic kinety 1 usually shortened, posterior end extending at about three fourths to four fifths of cell; oral apparatus typical of the genus, membranelle 1 clearly separated from other membranelles; freshwater and brackish water habitat. Deposition of voucher slides: Two voucher slides (registration nos. LMJ2015120701-1 and LMJ2015120701-2) have been deposited in Laboratory of Protozoology, Ocean University of China, Qingdao, China. Morphological description of Shenzhen population: Cell size in vivo about 30–40 μm × 12–20 μm. Cell shape elongate-elliptical in outline. Anterior end flat, with a prominent apical plate. Posterior part broadly rounded (Figs 2A, 3A–C, E). Buccal field about half body length and slightly concave. Pellicle thin and inconspicuously notched with ridges located longitudinally along ciliary rows (Figs 2A, 3A, E). No extrusomes detected in vivo. Cytoplasm colorless to slightly grayish, containing several bar-like crystals distributed in anterior and posterior portions. Well-fed individuals containing several to many grayish-green food vacuoles, leading to a dark gray body color at low magnifications (Figs 3A–E). Single contractile vacuole subcaudally positioned, about 3–4 μm in diameter when fully expanded, pulsating at intervals of 6–8 s (Figs 2A, 3A). Somatic cilia about 5–7 μm long in vivo, densely arranged (Figs 2A, 3A–E); single caudal cilium approximately 15–20 μm long (Figs 2A, 3A, C, D). Single spherical to oval macronucleus located centrally or slightly ahead of mid-body, about 10 μm in diameter in protargol preparations (Figs 2F, 3J–M). Locomotion by swimming moderately fast, but cells observed mostly crawling on substrates or resting on the bottom of petri dish when not disturbed. aCV, coefficient of variation in %; Max, maximum; Mean, arithmetic mean; Min, minimum; n, number of individuals examined; SD, standard deviation; SK 1, the kinety on right of buccal field; SK mid, the middle kinety on dorsal side; SK n, the kinety on left of buccal field. Somatic ciliature as shown in Figs 2C, F, 3F–M. Thirteen to fifteen somatic kineties (SKs) arranged longitudinally, forming a small glabrous area at anterior end (Figs 2C, F, 3J–M). Somatic kinety 1 (SK1, kinety on right of buccal field) usually shorter than other SKs, with posterior end terminating at about three fourths to four fifths of cell (Figs 2C, 3J, L). Somatic kinety n (SKn, kinety on left of buccal field) located slightly posteriorly with anterior end commencing at front part of membranelle 1 (M1) (Figs 2C, 3J, L). In general, each kinety composed of closely arranged dikinetids in anterior part and loosely arranged monokinetids posteriorly (Figs 2C, F, 3J–M). Dikinetids of some individuals extending to the posterior end, almost occupying four-fifths of SK. Somatic kinety 1 composed of 15–19 kinetids, including four to 14 dikinetids, while SKn composed of 15–20 kinetids, with three to 10 dikinetids (Figs 2C, 3J, L). The middle SK on the dorsal side comprising 12–15 kinetids (Figs 2F, 3K, M). Buccal apparatus similar to its congeners (Figs 2C, 3I, L). Membranelle 1 (M1) single-rowed and positioned near apical plate, clearly separated from other membranelles. It consisted of 5 or 6 basal bodies arranged in one row and a central basal body slightly deviated to the left (towards SKn) (Figs 2C, 3I, J, L). Membranelle 2 (M2) almost equal to M 1 in length and composed of two or three longitudinal rows of basal bodies (Figs 2C, 3H, I, L). Membranelle 3 (M3) composed of about seven to nine basal bodies, forming a small patch (Figs 2C, 3I, L). Paroral membrane (PM) on right of shallow buccal cavity, composed of two rows of basal bodies in a zigzag pattern, and extending anteriorly to about middle portion of M2 (Figs 2C, 3H–J, L). Scutica observed usually consisting of two or three pairs of basal bodies with one or two basal bodies positioned posteriorly (Figs 2C, 3F, G, L).Published as part of Liu, Mingjian, Li, Lifang, Qu, Zhishuai, Luo, Xiaotian, Al-Farraj, Saleh A., Lin, Xiaofeng & Hu, Xiaozhong, 2017, Morphological Redescription and SSU rDNA-based Phylogeny of Two Freshwater Ciliates, Uronema nigricans and Lembadion lucens (Ciliophora, Oligohymenophorea), with Discussion on the Taxonomic Status of Uronemita sinensis, pp. 17-37 in Acta Protozoologica 56 (1) on pages 19-21, DOI: 10.4467/16890027AP.17.003.6967, http://zenodo.org/record/836437