Rare Ciliate Research Articles

Ciliate diversity in rodrigo de freitas lagoon (Rio de Janeiro, Brazil) from an integrative standpoint.

The Rodrigo de Freitas Lagoon is a highly eutrophic lacustrine system and has one of the longest histories of exploration and anthropic alteration in Brazil. Despite its relevance, limited studies explored the diversity of micro-eukaryotes in the lagoon. Ciliates (Alveolata, Ciliophora) are overlooked in environmental microbiology, especially in tropical and subtropical ecosystems, resulting in limited knowledge about their diversity and functional relevance in South American habitats, particularly in coastal lagoons. To fill this gap, here we investigated the diversity of ciliates in a brackish coastal lagoon in an urban area of Rio de Janeiro, Brazil, applying and comparing the performance of morphological and metabarcoding approaches. The metabarcoding analysis, based on high-throughput sequencing of the hipervariable region V4 of the 18S rRNA genes detected 37 molecular operational taxonomic units (MOTUs) assigned to Ciliophora, representing only about a half (56.9%) of the diversity detected by microscopy, which counted 65 ciliate morphotypes. The most representative classes in both approaches were Spirotrichea and Oligohymenophorea. The metabarcoding analysis revealed that 35.3% of the ciliate MOTUs had less than 97% similarity to available sequences in the NCBI database, indicating that more than one-third of these MOTUs potentially represents still not represented or undescribed ciliate species in current databases. Our findings indicate that metabarcoding techniques can significantly enhance the comprehension of ciliate diversity in tropical environments, but the scarcity of reference sequences of brackish ciliates in molecular databases represents a challenge to the taxonomic assignment of the MOTUs. This study provides new insights into the diversity of ciliates in a threatened coastal lagoon, revealing a vast array of still unknown and rare ciliate taxonomic units in tropical environments.

Tracking down the rare ciliate biosphere

In protists, rare species include dormant organisms and those that do not reach high population abundance, and therefore, are not detected in the samples. These rare microorganisms are part of the so-called ‘rare microbial biosphere’. Although some may occasionally become abundant or dominant under particular environmental conditions, others do have a very rare occurrence, characterized by always having very low populations. The rare protist biosphere represents a significant component of microbial communities, and it is crucial for maintaining ecosystem biodiversity and function. In this study, we aim to demonstrate the richness of the rare ciliate biosphere and hypothesize on the reasons of rarity by combining morphological and ecological details on some exceedingly rare ciliates. The study includes the first report of different morphotypes of Dactylochlamys since 1928, first report of Penardiella undulata since 1930, second report of Penardiella interrupta since 1930, and an undescribed Penardiella species. The first report of Bryophyllum caudatum since 1933, microscopical observations and taxonomical discussion of the rare Legendrea bellerophon and of and undescribed Legendrea species. A new Apertospathula sp. with prokaryotic endosymbionts is described. The rarity of these species is explored and explained by their anaerobic metabolism combined with their prey selection.

The Extraordinarily Rare Ciliate Legendrea loyezae Fauré-Fremiet, 1908 (Haptoria, Ciliophora)

Diverse and dynamic communities of ciliates and other microbes thrive in the natural environment, driving the functioning of aquatic ecosystems. Many microbes are present in very low numbers or are dormant in the 'seedbank', escaping detection in environmental surveys and, consequently, remaining underexplored. Here, we report an extraordinarily rare ciliate that was discovered after persistent exploration of freshwater anoxic sediments - Legendrea loyezae Fauré-Fremiet, 1908, a member of the Family Spathidiidae, Order Haptorida. In this study, we present the sixth account of the ciliate since 1908 and reveal its phylogenetic position with the first 18S rRNA data for the genus. We explain the key morphological features of the species, describing a remarkable behaviour in which the ciliate "shapeshifts'' due to its ability of controlled full extension and retraction of its tube-like tentacles. Our results shed light on the similarity of L. loyezae to another ciliate that was first described as Legendrea bellerophon, later moved under a new genus and named Thysanomorpha bellerophon. We question the validity of this taxonomic decision and, based on morphological characters and tentacle movement, we propose moving T. bellerophon back under Legendrea. This study demonstrates how continued and persistent exploration of natural habitats lead to the discovery of microbial communities and species.

A new species of Trichodina lishuiensis n. sp. (Ciliophora: Trichodinidae) in urinary bladder of Odorrana schmackeri (Amphibia: Ranidae) from Zhejiang, China

Endoparasitic trichodinids are rather rare ciliates. In this study we describe a new species named Trichodina lishuiensis from the bladder of Odorrana schmackeri collected in Zhejiang, China, with the prevalence of 20% (9/45). We identified T. lishuiensis as a new species by morphological comparison and molecular analysis. The ciliates were observed using the dry-silver and protargol staining methods, as well as SEM (scanning electron microscopy). Trichodina lishuiensis is a small species (cell diameter 31.8-43.9 μm), with incompact denticles connection, medium-wide blades and thick rays. We also sequenced a 1712 bp-long fragment of the small subunit ribosomal RNA gene (SSU rRNA). Phylogenetic analyses showed that the new species clustered with Trichodina unionis. The route of transmission of Trichodina species in the urinary bladder remains a mystery. We hypothesize that the transmisison takes place during the amplexus, with eggs and sperm discharged from the cloaca, and that trichodinids ‘accompany’ the amphibian through its whole life cycle, but further studies are needed to test this hypothesis.

Distribution of Ciliates in Intertidal Sediments across Geographic Distances: A Molecular View

The estimation of the diversity and geographic distribution of protists in particular ciliates has long been an ongoing debate. We estimated the distribution of ciliates in intertidal sediments with geographic distance ranging from 10cm to 1,000km, using high-throughput DNA sequencing. Higher community similarity, in particular that of rare ciliate taxa, occurred between replicates than between sites. Statistical analyses showed that the community dissimilarities of both abundant and moderately abundant ciliates had correlations with geographic distance at the scales of 50m, 200km and 1000km, indicating a distance-decay relationship. No significant correlation was observed for rare taxa. The analysis of Bray-Curtis similarity showed a higher pairwise community similarity in abundant taxa than in moderately abundant taxa, and that in rare taxa was the lowest. Abundant taxa usually can disperse in a wider range than rare taxa, though their distribution is restricted by distance to some extent. Rare taxa are potentially more sensitive to changing environments, but no distance-decay relationship could be observed. The data indicate contrasting patterns of geographic distribution of the abundant and rare ciliate taxa and a weak distance-decay relationship for relatively abundant taxa at a scale over 50m.

Rare Freshwater Ciliate Paramecium chlorelligerum Kahl, 1935 and Its Macronuclear Symbiotic Bacterium "Candidatus Holospora parva".

Ciliated protists often form symbioses with many diverse microorganisms. In particular, symbiotic associations between ciliates and green algae, as well as between ciliates and intracellular bacteria, are rather wide-spread in nature. In this study, we describe the complex symbiotic system between a very rare ciliate, Paramecium chlorelligerum, unicellular algae inhabiting its cytoplasm, and novel bacteria colonizing the host macronucleus. Paramecium chlorelligerum, previously found only twice in Germany, was retrieved from a novel location in vicinity of St. Petersburg in Russia. Species identification was based on both classical morphological methods and analysis of the small subunit rDNA. Numerous algae occupying the cytoplasm of this ciliate were identified with ultrastructural and molecular methods as representatives of the Meyerella genus, which before was not considered among symbiotic algae. In the same locality at least fifteen other species of “green” ciliates were found, thus it is indeed a biodiversity hot-spot for such protists. A novel species of bacterial symbionts living in the macronucleus of Paramecium chlorelligerum cells was morphologically and ultrastructurally investigated in detail with the description of its life cycle and infection capabilities. The new endosymbiont was molecularly characterized following the full-cycle rRNA approach. Furthermore, phylogenetic analysis confirmed that the novel bacterium is a member of Holospora genus branching basally but sharing all characteristics of the genus except inducing connecting piece formation during the infected host nucleus division. We propose the name “Candidatus Holospora parva” for this newly described species. The described complex system raises new questions on how these microorganisms evolve and interact in symbiosis.

Morphology and ontogenesis of Stylonychia (Metastylonychia) nodulinucleata nov. subgen. (Ciliophora, Hypotricha) from Australia

Using standard methods, we describe the morphology and ontogenesis of a possibly very rare ciliate, Stylonychia (Metastylonychia) nodulinucleata nov. subgen (basionym: Stylonychia nodulinucleataShi and Li, 1993), isolated from soil of the Murray River floodplain in Australia. Further, we provide an English translation of the Chinese original description. Whether the Australian population is conspecific with the Chinese Stylonychia nodulinucleata requires a careful redescription of the latter. The new subgenus is characterized by a moniliform macronuclear strand and an ontogenetic feature, viz., that all cirri remain intact during anlagen formation. The moniliform macronuclear strand and the curved dorsal kineties resemble the stylonychid genus Coniculostomum. The species is easily recognized by the large size of the body and oral apparatus, the moniliform macronucleus, and the enormous caudal cirri reaching half of body length. Very likely, Stylonychia (Metastylonychia) nodulinucleata has a restricted distribution.

Ciliates and the rare biosphere-community ecology and population dynamics.

Application of deep sequencing technologies to environmental samples and some detailed morphological studies suggest that there is a vast, yet unexplored rare ciliate biosphere, tentatively defined in terms of operational taxonomic units. However, very few studies complemented molecular and phylogenetic data with morphological and ecological descriptions of the species inventory. This is mainly because the sampling effort increases strongly with decreasing species abundance. In spite of this limited knowledge, it is clear that species that are rare under certain environmental conditions (temporal rare biosphere) may become abundant when the physical, chemical, and biological variables of their habitat change. Furthermore, some species may always be present in low numbers if their dispersal rates are exceedingly high (accidental rare biosphere). An intriguing question is whether there are some species that are always rare, i.e., in every suitable environment. This permanent rare biosphere is conceptually different from the temporal rare biosphere. This review characterizes typical aquatic habitats of the rare ciliate biosphere, portrays different scenarios under which some or even many species may be permanently rare (background fauna), and identifies some fundamental questions that need to be addressed to achieve a better understanding of the population dynamics of the rare ciliate biosphere.

Optimization of DNA extraction from a single living ciliate for stable and repetitive PCR amplification

Ciliates are undoubtedly one of the most diverse protozoans that play a significant role in ecology. However, molecular examination, based on comparing the DNA sequences, has been done on a limited number of the species. Because most ciliates are uncultivable and their population sizes are often too small, it is usually difficult to obtain sufficient genomic DNA required for PCR based experiments. In the present study, we evaluated the effectiveness of four commercial DNA extraction procedures that extract high quality genomic DNA from a single ciliate cell. It was discovered that RED Extract‐N‐AmpTM PCR kit is the best method for removing PCR‐inhibiting substances and minimizing DNA loss during purification. This method can also amplify more than 25 reactions of PCR. In addition, this technique was applied to single cells of 19 species belonged to 7 orders under 5 classes that isolated from mixed natural populations. Their small subunit ribosomal DNA (SSU rDNA) was successfully amplified. In summary, we developed a simple technique for the high‐yield extraction of purified DNA from a single ciliate cell that may be more useful for rare ciliates, such as tiny and uncultivable marine microbes.

Role of soil in the life cycle of Meseres corlissi (Ciliophora: Oligotrichea): experiments with two clonal strains from the type locality, an astatic meadow pond

The life cycle of the oligotrich ciliate Meseres corlissi was investigated using 2 clonal strains, E4 and M10, which were isolated from soil samples collected at the type locality in Salzburg, Austria, and grown in a 1:1 mixture of WC medium and Eau de Volvic on a diet of cryptomonads. Growth, encystment, excystment and cyst survival of both strains depended strongly on the presence or absence of soil components in the culture medium. (1) Growth was enhanced greatly by addition of soil extract or sterilized garden soil. (2) Encystment could be induced by dilution of soil extract concentrations, whereas dilution of ciliates or food algae, at a constant soil extract level, had no significant effect. A sudden decrease in temperature, however, inhibited the encystment reaction. (3) Excystment could be triggered by addition of soil extract or sterilized garden soil. (4) Resting cysts survived desiccation periods of >7 d only in the presence of sterilized garden soil. The nature of the 'soil factor' responsible for these effects remains at present unknown. The growth and encystment responses of strains E4 and M10 differ clearly from those of the earlier investigated strain DR (Weisse 2004), which was isolated from the reservoir of a tree bromelia in the Dominican Republic. These dif- ferences are interpreted as local adaptations of 2 morphologically and genetically indistinguishable but geographically distant populations of a cosmopolitan but rare ciliate species.

Redescription of the rare marine ciliate, Prodiscocephalus borrori ( ) from shrimp-culturing waters near Qingdao, China, with redefinitions of the genera Discocephalus, Prodiscocephalus and Marginotricha (Ciliophora, Hypotrichida, Discocephalidae)

The morphology and infraciliature of the rare ciliate, Prodiscocephalus borrori (Wicklow, 1982) nov. comb. (formerly Psammocephalus borrori Wicklow, 1982), collected from a shrimp-culturing pond near Qingdao, China, were investigated by observing live and protargol-impregnated cells. Based on the information obtained from the previous and present work, an improved diagnosis for Prodiscocephalus Jankowski, 1979 is suggested: marine elongate to ovoid Discocephalidae with several unaligned and widely separated ventral cirri; both right and left marginal rows present, left marginal row divided into anterior and posterolateral parts; well-developed transverse cirri; caudal cirri present. At the same time, the genus, Psammocephalus Wicklow, 1982 is synonymized with Prodiscocephalus. Two related genera, Discocephalus Ehrenberg, 1828 and Marginotricha Jankowski, 1978 are redefined, and three new combinations, Marginotricha lithophora (Fauré-Fremiet, 1954) nov. comb., M. dragescoi (Wicklow, 1982) nov. comb. and M. faurei (Dragesco, 1963) nov. comb. are proposed.

Observations on a Rare Ciliate,Discomorphella pectinata(Levander, 1894) Corliss, 1960

ABSTRACT. Specimens of the rare ciliate Discomorphella pectinata (Levander, 1894) Corliss, 1960 were impregnated with silver nitrate in 1963. The body is discoid, about 60 μm long, laterally compressed and adorned with long spines. The somatic kineties on the right and left sides are sparse, sometimes disorganized, and locally without cilia. The oral zone has a complex infraciliature that lies above two series of ventral kineties and below a large, visor-like, epistomial fringe. The arrangement of this fringe is similar to that observed in some other heterotichous ciliates, notably members of the Metopidae and Caenomorphidae.

Observations on the life‐history of two rare ciliates, spathidium spathula and actinobolus radians

Observations on the life‐history of two rare ciliates, spathidium spathula and actinobolus radians