Molecular and morphological evidence for a sister group relationship of the classes Armophorea and Litostomatea (Ciliophora, Intramacronucleata, Lamellicorticata infraphyl. nov.), with an account on basal litostomateans

Single-cell transcriptomic analysis reveals genome evolution in predatory litostomatean ciliates

Many ciliated protists prey on other large microbial organisms, including other protists and microscopic metazoans. The ciliate class Litostomatea unites both predatory and endosymbiotic species. The evolution of predation ability in ciliates remains poorly understood, in part, due to a lack of genomic data. To fill this gap, we acquired the transcriptome profiles of six predatory litostomateans using single-cell sequencing technology and investigated their transcriptomic features. Our results show that: (1) in contrast to non-predatory ciliates, the predatory litostomateans have expanded gene families associated with transmembrane activity and reactive oxidative stress response pathways, potentially as a result of cellular behaviors such as fast contraction and extension; (2) the expansion of the calcium-activated BK potassium channel gene family, which hypothetically regulates cell contractility, is an ancient evolutionary event for the class Litostomatea, suggesting a rewired metabolism associated with the hunting behavior of predatory ciliates; and (3) three whole genome duplication (WGD) events have been detected in litostomateans, with genes associated with biosynthetic processes, transmembrane activity, and calcium-activated potassium channel activity being retained during the WGD events. In addition, we explored the evolutionary relationships among 17 ciliate species, including eight litostomateans, and provided a rich foundational dataset for future in-depth phylogenomic studies of Litostomatea. Our comprehensive analyses suggest that the rewired cellular metabolism via expanded gene families and WGD events might be the potential genetic basis for the predation ability of raptorial ciliates.

Comprehensive phylogenomic analyses reveal that order Armophorida is most closely related to class Armophorea (Protista, Ciliophora)

Ciliate species within the class Armophorea are widely distributed in various anaerobic environments, hence they are of great interest to researchers studying evolution and adaptation of eukaryotes to extreme habitats. However, phylogenetic relationships within the class remain largely elusive, most especially assignment of the order Armophorida and classification within the family Metopidae. In this study, we newly sequenced transcriptomes and the SSU rDNA of five armophorean species, Sulfonecta cf. uniserialis (order Armophorida), Nyctotheroides sp. (order Clevelandellida), and Metopus major, M. paraes, and Brachonella contorta (order Metopida). Comprehensive phylogenomic analyses revealed that Armophorea was most closely related to Muranotrichea and Parablepharismea. Our results indicate that the order Armophorida either belongs to Armophorea or represents a new class within APM (Armophorea-Parablepharismea-Muranotrichea). Analyses combining ecological niches and molecular trees showed that APM species might descend from an anaerobic free-living ciliate species. Existing molecular phylogenomic/phylogenetic and morphological evidence indicate that the family Metopidae is non-monophyletic and should be further classified with inclusion of additional lines of evidences. Our results provide new insights into the long-debated relationships within Armophorea.

Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental metabarcoding data. Here we fill this gap by providing reference alignments and trees for those ciliates taxa with available SSU-rDNA sequences derived from identified species. Each alignment contains 478 ciliate and six outgroup taxa, and they were made using different masking strategies for alignment positions (unmasked, masked and masked except the hypervariable V4 region). We constrained the monophyly of the major ciliate groups based on the recently updated classification of protists and based on phylogenomic data. Taxa of uncertain phylogenetic position were kept unconstrained, except for Mesodinium species that we constrained to form a clade with the Litostomatea. These ciliate reference alignments and trees can be used to perform taxonomic assignments of metabarcoding data, discover novel ciliate clades, estimate species richness, and overlay measured ecological parameters onto the phylogenetic placements.

A Phylogenomic Approach to Clarifying the Relationship of Mesodinium within the Ciliophora: A Case Study in the Complexity of Mixed-Species Transcriptome Analyses

Recent high-throughput sequencing endeavors have yielded multigene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multiprotein data set, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. Mesodinium always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of Mesodinium-M. rubrum, M. major, and M. chamaeleon-being more closely related to each other than to the heterotrophic member, M. pulex. The well-supported position of Mesodinium as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination-particularly for Mesodinium species where expression from stolen prey nuclei appears to dominate-requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.

A multigene timescale and diversification dynamics of Ciliophora evolution

Ciliophora is one of the most diverse lineages of unicellular eukaryotes. Nevertheless, a robust timescale including all main lineages and employing properly identified ciliate fossils as primary calibrations is lacking. Here, we inferred a time-calibrated multigene phylogeny of Ciliophora evolution, and we used this timetree to investigate the rates and patterns of lineage diversification through time. We implemented a two-step analytical approach that favored both gene and taxon sampling, reducing the uncertainty of time estimates and yielding narrower credibility intervals on the ribosomal-derived chronogram. We estimate the origin of Ciliophora at 1143 Ma, which is substantially younger than previously proposed ages, and the huge diversity explosion occurred during the Paleozoic. Among the current groups recognized as classes, Spirotrichea diverged earlier, its origin was dated at ca. 850 Ma, and Protocruziea was the younger class, with crown age estimated at 56 Ma. Macroevolutionary analysis detected a significant rate shift in diversification dynamics in the spirotrichean clade Hypotrichia + Oligotrichia + Choreotrichia, which had accelerated speciation rate ca. 570 Ma, during the Ediacaran-Cambrian transition. For all crown lineages investigated, speciation rates declined through time, whereas extinction rates remained low and relatively constant throughout the evolutionary history of ciliates.

EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates

High-throughput sequencing (HTS) surveys, among the most common approaches currently used in environmental microbiology, require reliable reference databases to be correctly interpreted. The EukRef Initiative (eukref.org) is a community effort to manually screen available small subunit (SSU) rRNA gene sequences and produce a public, high-quality and informative framework of phylogeny-based taxonomic annotations. In the context of EukRef, we present a database for the monophyletic phylum Ciliophora, one of the most complex, diverse and ubiquitous protist groups. We retrieved more than 11 500 sequences of ciliates present in GenBank (28% from identified isolates and 72% from environmental surveys). Our approach included the inference of phylogenetic trees for every ciliate lineage and produced the largest SSU rRNA tree of the phylum Ciliophora to date. We flagged approximately 750 chimeric or low-quality sequences, improved the classification of 70% of GenBank entries and enriched environmental and literature metadata by 30%. The performance of EukRef-Ciliophora is superior to the current SILVA database in classifying HTS reads from a global marine survey. Comprehensive outputs are publicly available to make the new tool a useful guide for non-specialists and a quick reference for experts.

Diversification dynamics of rhynchostomatian ciliates: the impact of seven intrinsic traits on speciation and extinction in a microbial group

Ciliates are a suitable microbial model to investigate trait-dependent diversification because of their comparatively complex morphology and high diversity. We examined the impact of seven intrinsic traits on speciation, extinction, and net-diversification of rhynchostomatians, a group of comparatively large, predatory ciliates with proboscis carrying a dorsal brush (sensoric structure) and toxicysts (organelles used to kill the prey). Bayesian estimates under the binary-state speciation and extinction model indicate that two types of extrusomes and two-rowed dorsal brush raise diversification through decreasing extinction. On the other hand, the higher number of contractile vacuoles and their dorsal location likely increase diversification via elevating speciation rate. Particular nuclear characteristics, however, do not significantly differ in their diversification rates and hence lineages with various macronuclear patterns and number of micronuclei have similar probabilities to generate new species. Likelihood-based quantitative state diversification analyses suggest that rhynchostomatians conform to Cope’s rule in that their diversity linearly grows with increasing body length and relative length of the proboscis. Comparison with other litostomatean ciliates indicates that rhynchostomatians are not among the cladogenically most successful lineages and their survival over several hundred million years could be associated with their comparatively large and complex bodies that reduce the risk of extinction.

Molecules illuminate morphology: phylogenomics confirms convergent evolution among 'oligotrichous' ciliates

'Oligotrichous' ciliates have been traditionally placed in a presumed monophyletic taxon called the Oligotrichia. However, gene sequences of the small subunit rRNA gene, and several other genes, suggest that the taxon is not monophyletic: although statistical support for this is not strong, the oligotrich Halteria grandinella is associated with the hypotrich ciliates and not with other oligotrich genera, such as Strombidium and Strombidinopsis. This has convinced some taxonomists to emphasize that morphological features strongly support the monophyly of the oligotrichs. To further test this hypothesis of monophyly, we have undertaken a phylogenomic analysis using the transcriptome of H. grandinella cells amplified by a single-cell technique. One hundred and twenty-six of 159 single-gene trees placed H. grandinella as sister to hypotrich species, and phylogenomic analyses based on a subset of 124 genes robustly rejected the monophyly of the Oligotrichia and placed the genus Halteria as sister to the hypotrich genera Stylonychia and Oxytricha. We use these phylogenomic analyses to assess the convergent nature of morphological features of oligotrichous ciliates. A particularly 'strong' morphological feature supporting monophyly of the oligotrichs is enantiotropic cell division, which our results suggest is nevertheless a convergent feature, arising through the need for dividing ciliates to undertake rotokinesis to complete cell division.

Evaluation of Systematic Position of Helicoprorodontids and Chaeneids (Ciliophora, Litostomatea): An Attempt to Break Long Branches in 18S rRNA Gene Phylogenies

Phylogenetic position of some free-living litostomatean taxa has not been correctly determined because of long-branch artifacts in 18S rRNA gene trees. The main aim of this study was to test the effectiveness of various masking algorithms, tree-building techniques, binarization of DNA data as well as combining morphological and molecular data to eliminate long-branch attraction of two problematic groups, helicoprorodontids and chaeneids. Guidance and SlowFaster masking in a combination with PhyloBayesian tree construction erased the artifactual positions of helicoprorodontids and chaeneids. On the other hand, binarization of DNA sequences and the strategy of combining morphological and molecular data eliminated only the artifactual position of chaeneids but not that of helicoprorodontids which were still being attracted by out-group taxa. According to statistical tree topology tests and comparative morphological studies, helicoprorodontids are classified as a distinct order while chaeneids are considered to be fast evolving members of the order Lacrymariida. The high body contractility, "cephalization" of the anterior body end, and helicalization of the anterior portion of some or all somatic ciliary rows indicate relatedness of helicoprorodontids, chaeneids, and lacrymariids. On the other hand, the dorsal brush separated from the circumoral kinety by dense ciliary files supports kinships of chaeneids, lacrymariids, and didiniids.

The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata)

The phylum Ciliophora plays important roles in a wide range of biological studies. However, the evolutionary relationships of many groups remain unclear due to a lack of sufficient molecular data. In this study, molecular dataset was expanded with representatives from 55 orders and all major lineages. The main findings are: (1) 14 classes were recovered including one new class, Protocruziea n. cl.; (2) in addition to the two main branches, Postciliodesmatophora and Intramacronucleata, a third branch, the Mesodiniea, is identified as being basal to the other two subphyla; (3) the newly defined order Discocephalida is revealed to be a sister clade to the euplotids, strongly suggesting the separation of discocephalids from the hypotrichs; (4) the separation of mobilids from the peritrichs is not supported; (5) Loxocephalida is basal to the main scuticociliate assemblage, whereas the thigmotrichs are placed within the order Pleuronematida; (6) the monophyly of classes Phyllopharyngea, Karyorelictea, Armophorea, Prostomatea, Plagiopylea, Colpodea and Heterotrichea are confirmed; (7) ambiguous genera Askenasia, CyclotrichiumParaspathidium and Plagiocampa show close affiliation to the well known plagiopyleans; (8) validity of the subclass Rhynchostomatia is supported, and (9) the systematic positions of Halteriida and Linconophoria remain unresolved and are thus regarded as incertae sedis within Spirotrichea.

Morphology and molecular phylogeny of a new haptorian ciliate, Chaenea mirabilis sp. n., with implications for the evolution of the dorsal brush in haptorians (Ciliophora, Litostomatea)

We discovered a new haptorian ciliate, Chaenea mirabilis sp. n., in brackish water collected near the town of Busan, Korea. Its morphology was studied using standard taxonomical methods and its phylogenetic relationships were assessed by phylogenetic analysis of the 18S rRNA gene. Chaenea mirabilis is distinguished from all congeners by the combination of the following traits: (i) a narrowly bursiform to flask-shaped, 60-100 μm long body; (ii) 11-21 doughnut-shaped or sometimes horseshoe-shaped macronuclear nodules; (iii) two types of extrusomes: type I is rod-shaped and 6-8 μm long, while type II is narrowly to broadly teardrop-shaped and only 1.5-2 μm long; (iv) highly refractive special granules tightly arranged between the first and second brush row, forming a conspicuous bulge; and (v) 12-13 somatic kineties. In the 18S rRNA gene phylogeny, C. mirabilis clustered with full support with other congeners. However, there was no statistical support for classification of Chaenea into the families Fuscheriidae, Acropisthiidae, or Trachelophyllidae, but a sister relationship with the Lacrymariidae could not be excluded. Therefore, we establish a new family, Chaeneidae, within the order Lacrymariida. This affiliation is strongly corroborated by the distinctly subapical dorsal brush bearing cilium-like bristles.

Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context

Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments.

Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data

The 18S rDNA phylogeny of Class Armophorea, a group of anaerobic ciliates, is proposed based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank database. Emphasis was placed on the use of two nucleotide alignment criteria that involved variation in the gap-opening and gap-extension parameters and the use of rRNA secondary structure to orientate multiple-alignment. A sensitivity analysis of 76 data sets was run to assess the effect of variations in indel parameters on tree topologies. Bayesian inference, maximum likelihood and maximum parsimony phylogenetic analyses were used to explore how different analytic frameworks influenced the resulting hypotheses. A sensitivity analysis revealed that the relationships among higher taxa of the Intramacronucleata were dependent upon how indels were determined during multiple-alignment of nucleotides. The phylogenetic analyses rejected the monophyly of the Armophorea most of the time and consistently indicated that the Metopidae and Nyctotheridae were related to the Litostomatea. There was no consensus on the placement of the Caenomorphidae, which could be a sister group of the Metopidae + Nyctorheridae, or could have diverged at the base of the Spirotrichea branch or the Intramacronucleata tree.

Morphology and morphogenesis of a soil ciliate, Rigidohymena candens (Kahl, 1932) Berger, 2011 (Ciliophora, Hypotricha, Oxytrichidae), with notes on its molecular phylogeny based on small-subunit rDNA sequence data

The morphology and morphogenesis of the stylonychine hypotrich Rigidohymena candens (Kahl, 1932) Berger, 2011, isolated from garden soil in Qingdao, China, were investigated using live observation and protargol impregnation methods. The Qingdao isolate possesses all diagnostic morphological characters of R. candens. The main events during binary fission are as follows: (i) the proter retains the parental adoral zone of membranelles entirely, whereas the old undulating membranes dedifferentiate into an anlage that gives rise to the leftmost frontal cirrus and the new undulating membranes of the proter; (ii) five streaks of fronto-ventral-transverse cirral anlagen are segmented in the pattern 3 : 3 : 3 : 4 : 4 from left to right, which form two frontal, four frontoventral, one buccal, five ventral and five transverse cirri, respectively; (iii) dorsal morphogenesis is in the typical Oxytricha pattern; (iv) three caudal cirri are formed, one at the posterior end of each of dorsal kineties 1, 2 and 4; and (v) the postoral ventral cirrus V/3 is not involved in primordia formation. The morphological and morphogenetic observations and phylogenetic analyses based on the small-subunit rDNA sequence data support the validity of Rigidohymena Berger, 2011 and its systematic position in the subfamily Stylonychinae.

Genealogical analyses of multiple loci of litostomatean ciliates (Protista, Ciliophora, Litostomatea)

The class Litostomatea is a highly diverse ciliate taxon comprising hundreds of free-living and endocommensal species. However, their traditional morphology-based classification conflicts with 18S rRNA gene phylogenies indicating (1) a deep bifurcation of the Litostomatea into Rhynchostomatia and Haptoria+Trichostomatia, and (2) body polarization and simplification of the oral apparatus as main evolutionary trends in the Litostomatea. To test whether 18S rRNA molecules provide a suitable proxy for litostomatean evolutionary history, we used eighteen new ITS1-5.8S rRNA-ITS2 region sequences from various free-living litostomatean orders. These single- and multiple-locus analyses are in agreement with previous 18S rRNA gene phylogenies, supporting that both 18S rRNA gene and ITS region sequences are effective tools for resolving phylogenetic relationships among the litostomateans. Despite insertions, deletions and mutational saturations in the ITS region, the present study shows that ITS1 and ITS2 molecules can be used to infer phylogenetic relationships not only at species level but also at higher taxonomic ranks when their secondary structure information is utilized to aid alignment.

Insights into the phylogeny of systematically controversial haptorian ciliates (Ciliophora, Litostomatea) based on multigene analyses

The ciliate subclass Haptoria is a diverse taxon that includes most of the free-living predators in the class Litostomatea. Phylogenetic study of this group was initially conducted using a single molecular marker small-subunit ribosomal RNA (SSU rRNA genes). Multi-gene analysis has been limited because very few other sequences were available. We performed phylogenetic analyses of Haptoria incorporating new SSU rRNA gene sequences from several debated members of the taxon, in particular, the first molecular data from Cyclotrichium. We also provided nine large-subunit ribosomal RNA (LSU rRNA) gene sequences and 10 alpha-tubulin sequences from diverse haptorians, and two possible relatives of controversial haptorians (Plagiopylea, Prostomatea). Phylogenies inferred from the different molecules showed the following: (i) Cyclotrichium and Paraspathidium were clearly separated from the haptorids and even from class Litostomatea, rejecting their high-level taxonomic assignments based on morphology. Both genera branch instead with the classes Plagiopylea, Prostomatea and Oligohymenophora. This raises the possibility that the well-known but phylogenetically problematic cyclotrichiids Mesodinium and Myrionecta may also have affinities here, rather than with litostomes; (ii) the transfer of Trachelotractus to Litostomatea is supported, especially by the analyses of SSU rRNA and LSU rRNA genes, however, Trachelotractus and Chaenea (more uncertainly) generally form the two deepest lineages within litostomes; and (iii) phylogenies of the new molecular markers are consistent with SSU rRNA gene information in recovering order Pleurostomatida as monophyletic. However, Pleurostomatida branches cladistically within order Haptorida, as does subclass Trichostomatia (on the basis of SSU rRNA phylogenies). Our results suggest that the class-level taxonomy of ciliates is still not resolved, and also that a systematic revision of litostomes is required, beginning at high taxonomic levels (taxa currently ranked as subclasses and orders).

Morphological and molecular phylogeny of dileptid and tracheliid ciliates: resolution at the base of the class Litostomatea (Ciliophora, Rhynchostomatia)

Dileptid and tracheliid ciliates have been traditionally classified within the subclass Haptoria of the class Litostomatea. However, their phylogenetic position among haptorians has been controversial and indicated that they may play a key role in understanding litostomatean evolution. In order to reconstruct the evolutionary history of dileptids and tracheliids, and to unravel their affinity to other haptorians, we have used a cladistic approach based on morphological evidence and a phylogenetic approach based on 18S rRNA gene sequences, including eight new ones. The molecular trees demonstrate that dileptids and tracheliids represent a separate subclass, Rhynchostomatia, that is sister to the subclasses Haptoria and Trichostomatia. The Rhynchostomatia are characterized by a ventrally located oral opening at the base of a proboscis that carries a complex oral ciliature. We have recognized two orders within Rhynchostomatia. The new order Tracheliida is monotypic, while the order Dileptida comprises two families: the new, typically bimacronucleate family Dimacrocaryonidae and the multimacronucleate family Dileptidae. The Haptoria evolved from the last common ancestor of the Litostomatea by polarization of the body, the oral opening locating more or less apically and the oral ciliature simplifying. The Trichostomatia originated from a microaerophylic haptorian by further simplification of the oral ciliature, possibly due to an endosymbiotic lifestyle.

Intraclass evolution and classification of the Colpodea (Ciliophora)

Using nine new taxa and statistical inferences based on morphological and molecular data, we analyze the evolution within the class Colpodea. The molecular and cladistic analyses show four well-supported clades: platyophryids, bursariomorphids, cyrtolophosidids, and colpodids. There is a widespread occurrence of homoplasies, affecting even conspicuous morphological characteristics, e.g. the inclusion of the micronucleus in the perinuclear space of the macronucleus. The most distinct changes in the morphological classification are the lack of a basal divergence into two subclasses and the split of the cyrtolophosidids into two main clades, differing mainly by the presence vs. absence of an oral cavity. The most complex clade is that of the colpodids. We partially reconcile the morphological and molecular data using evolutionary systematics, providing a scenario in which the colpodids evolved from a Bardeliella-like ancestor and the genus Colpoda performed an intense adaptive radiation, giving rise to three main clades: Colpodina n. subord., Grossglockneriina, and Bryophryina. Three new taxa are established: Colpodina n. subord., Tillinidae n. fam., and Ottowphryidae n. fam. Colpodean evolution and classification are far from being understood because sequences are lacking for most species and half of their diversity is possibly undescribed.