Morphology and ontogeny of Tetmemena pustulata indica nov. subspec. (Ciliophora, Hypotricha), from the Thane Creek, Mumbai, India

Polymorphism, gigantism, and cannibalism, one stylonychid ciliate (Ciliophora, Hypotricha) to rule them all

The morphology, ontogenesis, and molecular phylogeny of the polymorphic and cannibalistic giant forming Tetmemena polymorpha n. sp., found in a brackish water sample in South Korea, were investigated. The present species has long been misidentified as "Oxytricha bifaria." The new investigation shows that the species produces three morphologically different morphs. The small morph is bacterivorous and characterized by its small body size and slim body and it is found only in the stationary and decline phases of the culture. The large morph has a wide body, larger oral apparatus, and feeds on small eukaryotes such as yeast cells and small ciliates. It divides very quickly and produces the other two morphs and found in the exponential phase of the cultures. The giant morph is characterized by its huge body and oral apparatus. It feeds on the small morph cells of the same species and other ciliates, and occurs together with the small morph. Phylogenetic analyses based on the 18S rRNA gene sequences show that the new species is placed in a sister subclade to that containing other Tetmemena sequences. Moreover, Tetmemena indica Bharti et al., 2019 nov. stat. is raised to species level based on the differences in the cyst morphology and the dorsal ciliature to the authoritative Tetmemena pustulata population.

Free living ciliated protists from the chemoautotrophic cave ecosystem of Frasassi (Italy)

This study provides the first report on a community of free-living ciliated protists from the chemoautotrophic cave ecosystem of Frasassi, Italy. This subterranean groundwater ecosystem represents a hotspot of biodiversity that still needs to be fully explored with particular reference to microbial eukaryotes such as protist ciliates. A total of 33 taxa of ciliates were identified along with one species each of flagellate, heliozoans and naked amoebae, from four main sampling sites, namely, Grotta Solfurea (GSO), Lago Verde (LVE), Ramo Solfureo (RSO), and Pozzo dei Cristalli (PDC). The last consists of small microhabitats/ponds presenting different chemical–physical and biological parameters, such as sulfur and nutrient contents and the presence of bacterial biofilms. Furthermore, an analysis of the cryptic ciliate species biosphere as a ‘seedbank’ of diversity against cave ecosystem disturbance was also performed. This study also highlights some peculiar adaptations of cave-dwelling ciliates not described in their noncave-dwelling conspecifics, such as the extreme photosensitivity of Urocentrum turbo, the cannibalism of Coleps hirtus, the variable number of thorns in Aspidisca species as a defensive response to predation, and the frequent reorganization of ciliary structures in Euplotes aediculatus. The 18S rDNA sequences were generated for five species and were compared with those of the noncave-dwelling conspecifics. Finally, our results shed light on the still largely unknown ciliate diversity in the chemosynthesis-based sulfidic groundwater ecosystem of Frasassi.

Redescription of Bakuella (Bakuella) marina Agamaliev and Alekperov, 1976 (Protozoa, Hypotrichia), With Notes on Its Morphology, Morphogenesis, and Molecular Phylogeny

Because the original description of Bakuella (Bakuella) marina, type of the genus, is only based on protargol-impregnated specimens, one of the important living features, namely, the presence/absence of cortical granules, remains unknown so far. In the present work, a detailed investigation of a Chinese population of B. (Bakuella) marina is carried out using the integrated approaches, and the live morphology, ontogenesis, and molecular information of B. (Bakuella) marina are presented for the first time. The infraciliature of this population corresponds perfectly with that of the original description. The in vivo observation indicates that B. (Bakuella) marina possesses colorless cortical granules. The most prominent morphogenetic feature of B. (Bakuella) marina is that the parental adoral zone of membranelles is completely replaced by the newly formed one of the proters. Molecular phylogenetic analysis based on a small subunit ribosomal gene (SSU rDNA) shows that five Bakuella species are clustered with the species from other six Urostylid genera, namely, Anteholosticha, Apobakuella, Diaxonella, Holosticha, Neobakuella, and Urostyla. The monophyletic probabilities of the family Bakuellidae, genus Bakuella, subgenus B. (Bakuella), and subgenus B. (Pseudobakuella) are rejected by the approximately unbiased test. This study further shows that the family Bakuellidae, genus Bakuella, and subgenus B. (Bakuella) are all nonmonophyletic groups. In order to establish a reasonable classification system, information on molecular and morphogenesis of more Bakuellids and its related species is urgently needed.

Characterization of a Novel Hypotrich Ciliate From Heavy Metal-Contaminated Industrial Outlet in Onsan, Ulsan, South Korea

Very few studies exist on the description of protozoan ciliates from industrially contaminated sites. In this study, we report a description of a novel hypotrich ciliate isolated from water samples collected from an industrially contaminated outlet in Onsan, Ulsan, South Korea. The oxytrichid ciliate, Histriculus tolerans n. sp., was investigated using live observation and protargol impregnation. The morphology, morphogenesis, and molecular phylogeny inferred from small-subunit (SSU) rRNA gene sequences were studied. The new species is mainly characterized by a cell size of about 70 × 40 μm in vivo, two elongate ellipsoidal macronuclear nodules and one or two micronuclei, adoral zone of about 51% of body length with 32 membranelles on average, about 34 cirri in the right and 24 cirri in the left marginal row, 18 frontoventral transverse cirri, six dorsal kineties including two dorsomarginal rows, and dorsal kinety 1 with 26 bristles. Morphogenesis is similar to that of the type species, i.e., Histriculus histrio, except that oral primordium does not contribute to anlage II of the proter. Phylogenetic analyses, based on small-subunit rRNA gene sequences, consistently place the new species within the family Oxytrichidae, clustering with H. histrio.

Morphology, ontogeny and molecular phylogeny of a new urostylid ciliate, Bakuella (Pseudobakuella) guangdongica n. sp. (Ciliophora, Hypotrichia) from southern China

The morphology, morphogenesis, and molecular phylogeny of Bakuella (Pseudobakuella) guangdongica n. sp., isolated from southern China, were investigated. The new species is characterized by a body length of 150-225 μm in vivo; 35-42 adoral membranelles; 3-5 buccal, two frontoterminal, 7-12 transverse and two pretransverse ventral cirri; midventral complex comprised of 10-20 pairs and two rows extending to transverse cirri; posterior part of marginal rows slightly overlapping; colorless cortical granules about 1 μm across, arranged in small groups; soil habitat. Its main ontogenetic features are: (1) in the proter, the parental adoral zone of membranelles is completely renewed by new structures; (2) in the opisthe, the oral primordium originates apokinetally, some old midventral cirri join the formation of frontoventral-transverse cirral anlagen; (3) the anlagen for marginal rows and dorsal kineties develop intrakinetally; and (4) the numerous macronuclear nodules fuse into a single mass before dividing. Phylogenetic analyses based on the SSU rDNA sequence suggest the non-monophyly of the genus Bakuella.

New Contributions to the Diversity of Hypotrichous Ciliates: Description of a New Genus and Two New Species (Protozoa, Ciliophora)

Ciliated protists (ciliates) are extremely diverse and play important ecological roles in almost all kinds of habitats. In this study, two new hypotrichs, Wilbertophrya sinica n. g. and n. sp. and Bakuella xianensis n. sp., from China are investigated. Wilbertophrya n. g. can be separated from related genera mainly by the combination of lacking a buccal cirrus, pretransverse cirri, and caudal cirri, while possessing frontoterminal cirri. Analyses based on morphological and molecular data confirm the validity of the species, W. sinica n. sp., which is characterized as follows: body 50-115 μm × 15-35 μm in vivo; midventral complex comprises four or five cirral pairs only and terminates above mid-body; three frontal, two frontoterminal cirri, and two to four transverse cirri; about 15 macronuclear nodules; colorless cortical granules sparsely distributed. Another new species, B. xianensis n. sp., was isolated from a freshwater wetland and is defined as follows: body 115-150 μm × 40-65 μm in vivo; about 70 macronuclear nodules; dark-brownish cortical granules in groups; midventral complex comprises 8-12 cirral pairs forming a row that terminates posteriorly in mid-body region and two or three short midventral rows that are continuous with the row of midventral pairs; three frontal, four to six frontoterminal, and three to five fine transverse cirri; three bipolar dorsal kineties. Phylogenetic analyses based on small subunit ribosomal DNA (SSU rDNA) sequence data suggest that the new genus Wilbertophrya n. g. belongs to an isolated clade, which might represent an undescribed taxon at the family level, whereas B. xianensis n. sp. groups with several congeners and members of other related genera are within the core urostylids.

New contributions to the taxonomy of urostylid ciliates (Ciliophora, Hypotrichia), with establishment of a new genus and new species

Hypotrichia, one of the most complex and highly differentiated groups in Ciliophora, has been the object of extensive studies, especially in recent years. Nevertheless, methodological difficulties and insufficient faunistic studies have limited our understanding of their biodiversity and phylogeny. In this study, one novel urostylid ciliate, Pseudoholosticha zhaoi nov. gen., nov. spec. and two populations of Anteholosticha monilata (Kahl, 1928) Berger, 2003, type species of the latter genus, are studied using an integrative approach (live observation, protargol impregnation, scanning electron microscopy, and phylogenetic analysis) to provide further insights into the diversity, classification, and phylogeny of this group of ciliates. Pseudoholosticha nov. gen. can be separated from other morphologically similar genera mainly by the absence of buccal and caudal cirri. A key to 12 morphologically similar genera and illustrations of their cirral patterns are provided. The validation of the new genus and new species is supported by both morphological and phylogenetic analyses. The first 18S rRNA gene sequence of A. monilata, with detailed morphological data, provided a reliable clarification of A. monilata populations and corroborated the phylogenetic position of the type species of the polyphyletic genus Anteholosticha.

Molecular phylogeny of a new gonostomatid ciliate revealing a discrepancy between interphasic and cell divisional patterns (Ciliophora, Hypotricha)

The morphology, ontogenesis, and molecular phylogeny of a new ciliate, Gonostomum koreanum n. sp., discovered in a terrestrial moss sample from South Korea, were investigated. Morphologically, it is characterized by a gonostomatid oral apparatus, two macronuclear nodules, six frontoventral rows, the two rightmost of which (frontoventral rows V and VI) extend posteriorly to near pretransverse and transverse cirri, and three dorsal kineties each with a single caudal cirrus posteriorly. The new species is easily confused with members of the genus Metagonostomum because of the long frontoterminal cirral row but differs mainly in the de novo (vs. intrakinetal) origin of anlage VI, a character found only in Gonostomum and Paragonostomum. To solve the discrepancy between the interphasic and ontogenetic patterns, we additionally performed morphological and multigene analyses on three gonostomatid species, namely Gonostomum koreanum n. sp. and its morphologically (M. gonostomoida) and ontogenetically (G. kuehnelti) most similar species. The multigene analyses show that the new species is closely related to G. kuehnelti and the core gonostomatids consists of five groups based on the origin of the frontoventral rows.

Cell-division pattern and phylogenetic analyses of a new ciliate genus Parasincirra n. g. (Protista, Ciliophora, Hypotrichia), with a report of a new soil species, P. sinica n. sp. from northwest China

Background

Ciliated protists, a huge assemblage of unicellular eukaryotes, are extremely diverse and play important ecological roles in most habitats where there is sufficient moisture for their survivals. Even though there is a growing recognition that these organisms are associated with many ecological or environmental processes, their biodiversity is poorly understood and many biotopes (e.g. soils in desert areas of Asia) remain largely unknown. Here we document an undescribed form found in sludge soil in a halt-desert inland of China. Investigations of its morphology, morphogenesis and molecular phylogeny indicate that it represents a new genus and new species, Parasincirra sinica n. g., n. sp.

Results

The new, monotypic genus Parasincirra n. g. is defined by having three frontal cirri, an amphisiellid median cirral row about the same length as the adoral zone, one short frontoventral cirral row, cirrus III/2 and transverse cirri present, buccal and caudal cirri absent, one right and one left marginal row and three dorsal kineties. The main morphogenetic features of the new taxon are: (1) frontoventral-transverse cirral anlagen II to VI are formed in a primary mode; (2) the amphisiellid median cirral row is formed by anlagen V and VI, while the frontoventral row is generated from anlage IV; (3) cirral streaks IV to VI generate one transverse cirrus each; (4) frontoventral-transverse cirral anlage II generates one or two cirri, although the posterior one (when formed) will be absorbed in late stages, that is, no buccal cirrus is formed; (5) the posterior part of the parental adoral zone of membranelles is renewed; (6) dorsal morphogenesis follows a typical Gonostomum-pattern; and (7) the macronuclear nodules fuse to form a single mass. The investigation of its molecular phylogeny inferred from Bayesian inference and Maximum likelihood analyses based on small subunit ribosomal DNA (SSU rDNA) sequence data, failed to reveal its exact systematic position, although species of related genera are generally assigned to the family Amphisiellidae Jankowski, 1979. Morphological and morphogenetic differences between the new taxon and Uroleptoides Wenzel, 1953, Parabistichella Jiang et al., 2013, and other amphisiellids clearly support the validity of Parasincirra as a new genus. The monophyly of the family Amphisiellidae is rejected by the AU test in this study.

Conclusions

The critical character of the family Amphisiellidae, i.e., the amphisiellid median cirral row, might result from convergent evolution in different taxa. Amphisiellidae are not monophyletic.

Morphology, morphogenesis and molecular phylogeny of a novel soil ciliate, Afrokahliella paramacrostoma n. sp. (Ciliophora, Hypotrichia)

A soil hypotrich ciliate, Afrokahliella paramacrostoma n. sp., was discovered in China. Its morphology, morphogenesis and molecular phylogeny were investigated using standard methods. The new species is characterized as follows: body about 140-180 × 60-70 μm in vivo, cortical granules absent, contractile vacuole positioned about 40% down length of body, 5-9 macronuclear nodules, 34-49 adoral membranelles, 3-5 buccal and 3-6 parabuccal cirri, usually two frontoventral rows, three or four left and two or three right marginal rows, three dorsal kineties and one dorsomarginal kinety; 1-3 and one or two caudal cirri located at the ends of dorsal kineties 1 and 2, respectively. The ontogenetic process is characterized by: (1) the marginal anlagen on each side develop in the outer right and the inner left marginal rows, respectively; (2) five frontoventral-transverse cirral anlagen, anlagen II-IV develop in secondary mode; (3) dorsal morphogenesis follows a typical Urosomoida-pattern, no parental dorsal kineties are retained; (4) caudal cirri are generated at the ends of dorsal kineties 1 and 2. Phylogenetic analyses based on SSU rDNA sequence data reveals that Afrokahliella paramacrostoma n. sp. is closely related to Parakahliella macrostoma and Hemiurosomoida longa.

Morphology, Morphogenesis and Phylogenetic Position of the Soil Hypotrichous Ciliate, Parabistichella dieckmanni (Foissner, 1998) Foissner, 2016 (Ciliophora, Hypotrichia), with Notes on the Phylogeny of Parabistichella

The morphology, morphogenesis and molecular phylogeny of Parabistichella dieckmanni (Foissner, 1998) Foissner, 2016, isolated from north China, were investigated. The Chinese population was characterized as having five to seven frontal cirri in corona, four to seven buccal cirri arranged in a row, two to four short frontal rows and two long frontoventral rows, three to seven transverse cirri, four macronuclear nodules, three dorsal kineties following a Gonostomum-pattern, and caudal cirri absent. Morphogenetic research reveals that the main characteristics during binary fission are as follows: (1) the long left frontoventral row is formed by two or three anlagen; (2) the posterior part of the parental adoral zone of membranelles is renewed, and the oral primordium of the opisthe is formed intrakinetally; (3) FVT-anlagen I to VI (or V, VII) produce each a frontal cirrus to form the frontal corona; (4) development of dorsal kineties follows the Gonostomum-pattern. Phylogenetic analyses showed that P. dieckmanni does not group with other Parabistichella species. Therefore, the genus Parabistichella is polyphyletic. Additionally, Parabistichella variabilis n. comb. (basionym: Bistichella variabilis He & Xu, 2011) and Parabistichella cheni n. nom. (basionym: Parabistichella variabilis Jiang et al., 2013) were suggested.

Description and Morphogenesis of a Chinese Population of Bakuella granulifera Foissner, Agatha and Berger, 2002 (Ciliophora, Hypotricha)

In this study, the morphology and morphogenesis of Bakuella granulifera Foissner, Agatha, and Berger, 2002, isolated from soil in the Chanba National Wetland Park, Xi'an, China, were studied based on in vivo observations and protargol staining. The Chinese population is distinctly smaller than the type population from Namibia. Details of the ontogenetic process are provided for the first time and are summarized as follows: (1) the parental adoral zone is partly retained; (2) the left of the endoral forms a rather wide anlage and the proximal adoral membranelles are renewed; (3) the parental midventral complex contributes to the formation of the FVT cirral anlagen; (4) the marginal rows anlagen and dorsal kineties anlagen develop intrakinetally; (5) no caudal cirri are produced; and (6) the macronuclear nodules fuse to a single mass. In combination with previous studies, these findings suggest that the genus Bakuella is ontogenetically diverse.

Assessing the utility of Hsp90 gene for inferring evolutionary relationships within the ciliate subclass Hypotricha (Protista, Ciliophora)

BACKGROUND

Although phylogenomic analyses are increasingly used to reveal evolutionary relationships among ciliates, relatively few nuclear protein-coding gene markers have been tested for their suitability as candidates for inferring phylogenies within this group. In this study, we investigate the utility of the heat-shock protein 90 gene (Hsp90) as a marker for inferring phylogenetic relationships among hypotrich ciliates.

RESULTS

A total of 87 novel Hsp90 gene sequences of 10 hypotrich species were generated. Of these, 85 were distinct sequences. Phylogenetic analyses based on these data showed that: (1) the Hsp90 gene amino acid trees are comparable to the small subunit rDNA tree for recovering phylogenetic relationships at the rank of class, but lack sufficient phylogenetic signal for inferring evolutionary relationships at the genus level; (2) Hsp90 gene paralogs are recent and therefore unlikely to pose a significant problem for recovering hypotrich clades; (3) definitions of some hypotrich orders and families need to be revised as their monophylies are not supported by various gene markers; (4) The order Sporadotrichida is paraphyletic, but the monophyly of the "core" Urostylida is supported; (5) both the subfamily Oxytrichinae and the genus Urosoma seem to be non-monophyletic, but monophyly of Urosoma is not rejected by AU tests.

CONCLUSIONS

Our results for the first time demonstrate that the Hsp90 gene is comparable to SSU rDNA for recovering phylogenetic relationships at the rank of class, and its paralogs are unlikely to pose a significant problem for recovering hypotrich clades. This study shows the value of careful gene marker selection for phylogenomic analyses of ciliates.

Taxonomic resolution of Stylonychia notophora (Alveolata, Ciliophora, Hypotricha) sensu Sapra and Dass 1970 using an integrative approach

The spirotrichean ciliate Stylonychia notophora has previously been recorded in India although the descriptions are lacking in detail. It has been suggested several times that the Indian population, S. notophora sensu Sapra and Dass, 1970 collected along the Delhi stretch of the River Yamuna, is identical to Tetmemena pustulata, but this has never been confirmed due to insufficient data for the former. The present study includes detailed descriptions (classical and molecular) of populations of Tetmemena isolated from six locations along the River Yamuna, India. These include four from the Delhi stretch including that from which Sapra and Dass, 1970 isolated their population of S. notophora. Due to the lack of a sufficiently detailed description, the taxonomic status of S. notophora sensu Sapra and Dass, 1970 was not clear. Comparisons among the populations isolated in the present study with previous descriptions of T. pustulata and S. notophora sensu Sapra and Dass, 1970 show only minor differences in morphometry, morphogenesis and in 18S rDNA sequences. The 18S rDNA sequences of all six populations had 99% similarity to both T. pustulata and S. notophora. These findings support the contention that S. notophora sensu Sapra and Dass, 1970 was misidentified and is a population of T. pustulata. This study supports the need for adopting an integrative approach based on morphological, morphogenetic and molecular data in order to understand species delimitation in ciliated protists.

Morphogenesis and molecular phylogeny of two soil ciliates Australocirrus australis (Foissner, 1995) Kumar and Foissner, 2015 and A. aspoecki (Foissner, 2004) Kumar and Foissner, 2015 (Ciliophora, Hypotrichia)

The morphogenesis and molecular phylogeny of two soil hypotrich ciliates, Australocirrus australis and A. aspoecki, collected from Xi'an, Shaanxi Province, China, were investigated using protargol preparation. The main features of morphogenesis of A. australis are as follows: (1) the parental adoral zone of membranelles is retained completely in the proter; (2) parental cirri and the undulating membranes are involved in the formation of six primordial streaks; (3) multiple fragmentation of the third dorsal kinety anlage; (4) more than three dorsomarginal kineties are formed. An early divider of A. aspoecki was also found, and its morphogenetic events resemble those of other Australocirrus species. Furthermore, the SSU rDNA sequence of the Shaanxi populations of A. australis and A. aspoecki was provided. The molecular phylogeny indicates that A. aspoecki clusters together with A. rubrus and two populations of A. australis with full support, which are separated from the clade comprising the two populations of A. shii.