Systematic Redefinition of the Hypotricha (Alveolata, Ciliophora) Based on Combined Analyses of Morphological and Molecular Characters

Investigating non-fungal eukaryotic diversity in snow in the Antarctic Peninsula region using DNA metabarcoding

Snow is a unique microhabitat, despite being a harsh environment, multiple life forms have adapted to survive in it. While algae, bacteria and fungi are dominant microorganisms in Antarctic snow, little is known about other organisms that may be present in this habitat. We used metabarcoding to investigate DNA sequence diversity of non-fungal eukaryotes present in snow obtained from six different sites across the Maritime Antarctica. A total of 20 taxa were assigned to obtained sequences, representing five Kingdoms (Chromista, Protozoa, Viridiplantae and Metazoa) and four phyla (Ciliophora, Cercozoa, Chlorophyta and Cnidaria). The highest diversity indices were detected in Trinity Peninsula followed by Robert Island, Arctowski Peninsula, Deception Island, King George Island and Snow Island. The most abundant assignments were to Trebouxiophyceae, followed by Chlamydomonas nivalis and Chlamidomonadales. No taxa were detected at all sites. Three potentially new records for Antarctica were detected: two Ciliophora (Aspidisca magna and Stokesia sp.) and the green algae Trebouxia potteri. Our data suggested that similarities found between the sites may be more related with snow physicochemical properties rather than geographic proximity or latitude. This study provides new insights into the diversity and distribution of eukaryotic organisms in Antarctic snow.

Morphological, ontogenetic, and phylogenetic research of a poorly known non-dorsomarginalian ciliate: Erniella filiformis Foissner, 1987 (Protista, Ciliophora, Hypotrichia)

Erniella Foissner, 1987 is a poorly known genus with its available information limited solely to morphological characteristics. In this study, the type species E. filiformis, isolated from highly saline water in China, was investigated for morphology, morphogenesis, and phylogeny based on small subunit ribosomal DNA sequences. The main characteristic events during morphogenesis in Erniella filiformis are as follows: (1) in the proter, only the posterior part of the parental adoral zone is renewed and undulating membranes anlage is formed from the dedifferentiation of the old structure; (2) the oral primordium is formed intrakinetally in the opisthe; (3) frontoventral-transverse cirral anlagen II-IV develop in the primary mode, anlage V develops intrakinetally in the proter; and (4) the right frontoventral row is formed by a single anlage. The phylogenetic analyses indicate that Erniella forms a monophyletic group with Bistichella, Keronopsis, Lamtostyla, Orthoamphisiella, Parabistichella, Paraholosticha, and Uroleptoides.

Ciliate Morpho-Taxonomy and Practical Considerations before Deploying Metabarcoding to Ciliate Community Diversity Surveys in Urban Receiving Waters

Disentangling biodiversity and community assembly effects on ecosystem function has always been an important topic in ecological research. The development and application of a DNA metabarcoding method has fundamentally changed the way we describe prokaryotic communities and estimate biodiversity. Compared to prokaryotes (bacteria and archaea), the eukaryotic microbes (unicellular eukaryotes) also fulfill extremely important ecological functions in different ecosystems regarding their intermediate trophic positions. For instance, ciliated microbes (accounting for a substantial portion of the diversity of unicellular eukaryotes) perform pivotal roles in microbial loops and are essential components in different ecosystems, especially in water purification processes. Therefore, the community composition of ciliated species has been widely utilized as a proxy for water quality and biological assessment in urban river ecosystems and WWTPs (wastewater treatment plants). Unfortunately, investigating the dynamic changes and compositions in ciliate communities relies heavily on existing morpho-taxonomical descriptions, which is limited by traditional microscopic approaches. To deal with this dilemma, we discuss the DNA-based taxonomy of ciliates, the relative merits and challenges of deploying its application using DNA metabarcoding for surveys of ciliate community diversity in urban waterbodies, and provide suggestions for minimizing relevant sources of biases in its implementation. We expect that DNA metabarcoding could untangle relationships between community assembly and environmental changes affecting ciliate communities. These analyses and discussions could offer a replicable method in support of the application of evaluating communities of ciliated protozoa as indicators of urban freshwater ecosystems.

Hypotrichidium tisiae (Gelei, 1929) Gelei, 1954: a unique hypotrichid ciliate having a highly specialized developmental pattern during binary division

In sharp contrast to their pelagic relatives, the oligotrichs, the overwhelming majority of hypotrich ciliates inhabit the benthos. Only a few species, including those of the genus Hypotrichidium Ilowaisky, 1921, have adapted to a planktonic lifestyle. The ontogenetic mode of the highly differentiated ciliate, Hypotrichidium tisiae (Gelei, 1929) Gelei, 1954, is unknown. In this study, the interphase morphology and the ontogenetic process of this species are investigated. Accordingly, the previously unidentified ciliary pattern of Hypotrichidium is redefined. The main morphogenetic features are as follows: (1) The parental adoral zone of membranelles is inherited completely by the proter and the oral primordium of the opisthe arises in a deep pouch. (2) Five frontoventral cirral anlagen (FVA) are formed: FVA I contributes to the single frontal cirrus, FVA II-IV generate three frontoventral cirral rows, FVA V migrates and forms postoral ventral cirri. (3) All marginal cirral row anlagen develop de novo: each of the two left anlagen forms a single cirral row, while the single right anlage fragments into anterior and posterior parts. (4) Two dorsal kinety anlagen occur de novo, with the right one fragmenting to form kineties 2 and 3. (5) Two long caudal cirral rows are formed at the ends of dorsal kineties 1 and 3. On the basis of the morphogenetic features and phylogenetic analyses, the assignment of Hypotrichidium to the family Spirofilidae Gelei, 1929 within Postoralida is supported. The establishment of separate families for the slender "tubicolous" spirofilids and the highly helical spirofilids is also validated.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00148-9.

Biodiversity of freshwater ciliates (Protista, Ciliophora) in the Lake Weishan Wetland, China: the state of the art

Ciliates are core components of the structure of and function of aquatic microbial food webs. They play an essential role in the energy flow and material circulation within aquatic ecosystems. However, studies on the taxonomy and biodiversity of freshwater ciliates, especially those in wetlands in China are limited. To address this issue, a project to investigate the freshwater ciliates of the Lake Weishan Wetland, Shandong Province, commenced in 2019. Here, we summarize our findings to date on the diversity of ciliates. A total of 187 ciliate species have been found, 94 of which are identified to species-level, 87 to genus-level, and six to family-level. These species show a high morphological diversity and represent five classes, i.e., Heterotrichea, Litostomatea, Prostomatea, Oligohymenophorea, and Spirotrichea. The largest number of species documented are oligohymenophoreans. A comprehensive database of these ciliates, including morphological data, gene sequences, microscope slide specimens and a DNA bank, has been established. In the present study, we provide an annotated checklist of retrieved ciliates as well as information on the sequences of published species. Most of these species are recorded in China for the first time and more than 20% are tentatively identified as new to science. Additionally, an investigation of environmental DNA revealed that the ciliate species diversity in Lake Weishan Wetland is higher than previously supposed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00154-x.

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.

Insights into the phylogeny of the family Deviatidae (Protozoa, Ciliophora, Hypotrichia) based on multi-gene, morphological and ontogenetic information, with the establishment of a new species Deviata multilineae n. sp

Hitherto, the phylogeny of ciliated protists, an important group of model organisms in many fields, has been mainly based on a single marker gene (SSU rDNA, nuclear small subunit ribosomal RNA gene). However, there is increasing evidence showing this is insufficient to provide robust phylogenies and has resulted in confusing systematics in many ciliates groups. Among these, the phylogenies within family Deviatidae (Spirotrichea, Hypotrichia) are ambiguous due to the dependence on SSU rDNA and undersampling. Here, we provide eight new sequences and conduct phylogenetic analyses based on both multi-gene and single-gene to clarify evolutionary relationships among all deviatids for which gene sequence are available. The results reveal that: (1) the monophyly of Deviatidae is well-supported by both single-gene and concatenated data; (2) the presence of fine cirri and relatively wide spacing of these cirri within all rows are plesiomorphies of Deviatidae; (3) Pseudosincirra longicirrata is closely related to Deviata rositae, which is supported by their shared possession of dorsomarginal kineties; (4) phylogenetic analyses and approximately unbiased test based on multi-gene support a close relationship among taxa lacking dorsomarginal kineties (D. parabacilliformis, D. multilineae nov. spec., D. abbrevescens, D. brasiliensis and Perisincirra paucicirrata); (5) Deviatidae shows a close relationship with Dorsomarginalia and Strongylidium-Hemiamphisiella-Pseudouroleptus assemblage, suggesting the presence/absence of dorsomarginal kineties is phylogenetically informative in this family and presence of them may be a plesiomorphy. Based on the morphological, morphogenetic and phylogenetic data, the evolutionary relationships within Deviatidae are hypothesized, and a new ciliate, Deviata multilineae nov. spec., collected from China, is investigated.

Multi-Gene Phylogeny of the Ciliate Genus Trachelostyla (Ciliophora, Hypotrichia), With Integrative Description of Two Species, Trachelostyla multinucleata Spec. nov. and T. pediculiformis (Cohn, 1866)

Many hypotrich genera, including Trachelostyla, are taxonomically challenging and in a need of integrative revision. Using morphological data, molecular phylogenetic analyses, and internal transcribed spacer 2 (ITS2) secondary structures, we attempt to cast more light on species relationships within the genus Trachelostyla. The present multifaceted approach reveals that (1) a large-sized species with numerous macronuclear nodules, isolated from sandy littoral sediments in southern China, is new to science and is endowed here with a name, T. multinucleata spec. nov.; (2) two other Chinese populations previously identified as T. pediculiformis represent undescribed species; and (3) multigene phylogeny is more robust than single-gene trees, recovering the monophyly of the genus Trachelostyla with high bootstrap frequency. Additionally, ITS2 secondary structures and the presence of compensatory base changes in helices A and B indicate the presence of four distinct taxa within the molecularly studied members of the genus Trachelostyla. Molecular data are more suitable for delimitation of Trachelostyla species than morphological characters as interspecific pairwise genetic distances of small subunit (18S) rDNA, ITS1-5.8S-ITS2, and large subunit (28S) rDNA sequences do not overlap, whereas ranges of multiple morphometric features might transcend species boundaries.

Phylogeny of a new ciliate family Clampidae fam. nov. (Protista: Ciliophora), with notes on morphology and morphogenesis

Hypotrichs comprise a highly differentiated and diversified group of ciliates with an evolutionary history characterized by an exceptional number of convergences and reversions. A new hypotrich ciliate from a freshwater fishpond is investigated based on morphological, morphogenetic and molecular data. The phylogenetic analyses reveal that the new species is closely related to Simplicitergida despite the absence of zigzag-patterned midventral cirral pairs, a common feature of simplicitergids. The phylogenetic position of this atypical simplicitergid species is strongly supported by the conserved features of dorsal ciliature and nuclear apparatus, which are probably more informative than cirral patterns for higher-rank classification. The close phylogenetic relationships among those Simplicitergida with varied cirral patterns could be explained by evolutionary convergences and reversions. The new species is recognized mainly by three frontoventral rows, several short midventral rows, two long midventral rows and the absence of zigzag-patterned midventral cirral pairs. Based on comprehensive phylogenetic analyses, together with detailed morphological and morphogenetic comparisons, a new family, Clampidae fam. nov., is proposed for the new genus and species, Clampia sinica gen. et sp. nov. In addition, an emended diagnosis of the morphologically similar family Epiclintidae is provided.

Redescription, Morphogenesis, and Molecular Phylogeny of Pseudosincirra longicirrata nov. comb., With Establishment of a New Genus Pseudosincirra nov. gen. (Ciliophora, Hypotrichia)

The morphology and morphogenesis of Pseudosincirra longicirrata nov. gen. and nov. comb., isolated from southern China, were investigated with living observation and protargol staining. Our population is similar to the original population in living characteristics and ciliary patterns. The main determinable morphogenetic features of P. longicirrata nov. comb. are the presence of five frontoventral-transverse cirral anlagen (FVT-anlagen) and a dorsomarginal kinety anlage. According to the origin of FVT-anlagen IV and V in proter, it can be determined that P. longicirrata nov. comb. possesses two frontoventral rows and one right marginal row. Hence, a new genus, Pseudosincirra nov. gen., is proposed, and the diagnosis of P. longicirrata nov. comb. is improved. The new genus is diagnosed as follows: adoral zone of membranelles and undulating membranes is in a Gonostomum pattern; there are three enlarged frontal cirri, one buccal cirrus, and one parabuccal cirrus; postperistomial cirrus and transverse cirri are lacking; there are two more or less long frontoventral rows and one right and two or more left marginal rows; cirri within all rows very widely spaced; dorsal kinety pattern is of Urosomoida type, that is, three dorsal kineties and one dorsomarginal kinety; and caudal cirri are present. Phylogenetic analyses based on the small subunit ribosomal (SSU rDNA) sequence data indicate that P. longicirrata nov. comb. clusters with Deviata and Perisincirra. It is considered that Pseudosincirra nov. gen. and Perisincirra paucicirrata should be assigned to the family Deviatidae; fine cirri, and cirri within all rows being relatively widely spaced, should be considered as plesiomorphies of Deviatidae; and Deviatidae is closely related to Dorsomarginalia or Strongylidium-Hemiamphisiella-Pseudouroleptus.

A putatively extinct higher taxon of Spirotrichea (Ciliophora) from the Lower Cretaceous of Brazil

Fossil microeukaryotes are key elements for understanding ancient ecosystems at microscopic level and improving the knowledge on the diversification of microbial life as a whole. We describe Palaeohypothrix bahiensis gen. et sp. nov., an exceptionally well-preserved Lower Cretaceous (Berriasian-Barremian; 145-125 Mya) amber-entrapped microeukaryote, identified as a spirotrich ciliate. The preservation of structures interpreted as the nuclear apparatus and remains of the ciliature revealed a novel ground plan, not found in modern Spirotrichea, thus representing a putatively extinct higher taxon lineage, viz. the Palaeohypotricha nov. tax. Based on cladistic analysis, the new taxon is hypothesized as phylogenetically related to the Protohypotrichia.

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.

A new hypotrich ciliate, Oxytricha xianica sp. nov., with notes on the morphology and phylogeny of a Chinese population of Oxytricha auripunctata Blatterer & Foissner, 1988 (Ciliophora, Oxytrichidae)

The morphology and infraciliature of the new hypotrichous ciliate, Oxytricha xianica sp. nov., and a Chinese population of Oxytricha auripunctata Blatterer & Foissner, 1988, are investigated using live observation and protargol staining. Oxytricha xianica sp. nov. is defined by the body size 85-130 µm × 30-50 µm in vivo, the typical oxytrichid 18 frontoventral-transverse cirri, cortical granules absent, undulating membranes reduced or absent, three caudal cirri, dorsal kineties in Oxytricha pattern, and two ellipsoidal macronuclear nodules. The Chinese population of O. auripunctata differs slightly from other populations in the arrangement and color of cortical granules and position of anterior end of dorsal kinety 4. Phylogenetic analyses based on SSU-rDNA sequences support the assertion that O. auripunctata belongs to Oxytricha and Oxytrichidae.

Taxonomy and Molecular Phylogeny of Two New Urostylid Ciliates (Protozoa: Ciliophora) From Chinese Wetlands and Establishment of a New Genus

Hypotrich ciliates with evolutionary novelties are continually being discovered, challenging the current taxonomic system and attracting increased attention. In the present work, two new urostylid ciliates, Heterobakuella bergeri gen. nov., sp. nov. and Anteholosticha perezuzae sp. nov., isolated from Chinese wetland samples, were identified based on morphology and 18S rRNA gene sequences. Heterobakuella gen. nov. is defined by three frontal cirri, single buccal cirrus, one parabuccal cirrus, midventral complex composed of cirral pairs and one cirral row, one left and two right marginal cirral rows, transverse and pretransverse cirri present, caudal and frontoterminal cirri absent. Heterobakuella can be easily distinguished from the morphologically most similar genus, Apobakuella, mainly by the single buccal cirrus (vs. one buccal cirral row) and one parabuccal cirrus (vs. several parabuccal cirral rows originated from different anlagen). Phylogenetic analyses show that H. bergeri branches within the clade formed by Bergeriella ovata, Monocoronella carnea, Anteholosticha gracilis, and Neourostylopsis spp., rather than the clade represented by Apobakuella. The other species, A. perezuzae, is mainly characterized by a distinctly slender body shape with an average length:width ratio about 7, distinctively shaped biconcave and greenish cortical granules, as well as one or two pretransverse cirri. Phylogenetic analyses indicate the genus Anteholosticha is non-monophyletic.

Morphology, Morphogenesis, and Molecular Phylogeny of a New Freshwater Ciliate, Quadristicha subtropica n. sp. (Ciliophora, Hypotrichia)

The morphology and the regulation of cortical pattern associated with the cell size, division, and phylogenetic position of a new hypotrichous ciliate, Quadristicha subtropica n. sp. collected from a freshwater pond in southern China, were investigated. Quadristicha subtropica n. sp. is characterized as follows: size in vivo 60-115 μm × 25-45 μm; 19-21 adoral membranelles; buccal cirrus near anterior end of endoral and paroral; cirrus IV/3 at about level of buccal vertex; right marginal row begins ahead of buccal vertex; 11-16 right and 12-19 left marginal cirri; and dorsal cilia about 5 μm long. The basic morphogenetic process in Q. subtropica n. sp. is consistent with that of the type species, Quadristicha setigera. Phylogenetic analyses based on small subunit ribosomal DNA sequence data reveal that the systematic position of Q. subtropica n. sp. is rather unstable with low support values across the tree and the genus Quadristicha is not monophyletic.

Tunicothrix halophila n. sp., a Secondarily Oligomerized Parabirojimid Hypotrich (Ciliophora, Spirotrichea) From Hypersaline Costal Water in Korea

Tunicothrix halophila n. sp. was discovered in a hypersaline marine sample from Jeju Island, Korea. It is characterized by the highly reduced number of dorsal bristles. In addition, the main character of the genus Tunicothrix (e.g., alveolar layer) is absent/indistinct. To figure out its identity and phylogenetic relationship, we examined the new species based on modern morphological methods and molecular phylogenetic analyses. Since the parabirojimids are of basal position to core hypotrichs and a smaller data set could show incorrect phylogenetic relationships among the hypotrichs, we used a huge data set composed of 1,460 DNA sequences to infer the phylogenetic tree. The reduction of dorsal bristles is very likely a secondarily evolved character in hypotrichs, resulting in the independent phenotypic adaptation in the hypersaline ecosystems as shown in other hypersaline hypotrichs. Furthermore, the so-called right marginal row 1 in other congeners is found to produce a pretransverse and transverse cirrus and thus we recommend using the term frontoventral row. Based on our data, we can justify Tunicothrix halophila n. sp. as a new species; however, despite the phenotypic distinctiveness, we refrain to establish a new genus because of the missing data and the non-monophyly of Tunicothrix.

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.