Further consideration of the phylogeny of some "traditional" heterotrichs (Protista, Ciliophora) of uncertain affinities, based on new sequences of the small subunit rRNA gene

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.

The widely reported but poorly studied ciliate family Folliculinidae (Protozoa, Ciliophora, Heterotrichea): a revision with notes on its taxonomy, morphology and phylogenetic relationships

Ciliates of the heterotrich family Folliculinidae are widespread in various habitats and are distinguished by their transparent loricae of various shapes, conspicuous peristomial lobes, and dimorphic life cycles. They usually attach firmly to the surface of substrates, feed on bacteria and microalgae, and play a significant role in energy flow and material cycling in the microbial food web. However, little is known regarding their biodiversity and systematics. In this work, we establish the terminology of the family Folliculinidae and select six crucial features for genus recognition. Based on previous studies, we revise the classification of Folliculinidae, supply improved diagnoses for each of the 33 folliculinid genera, and provide a key to their identification. Moreover, phylogenetic analyses based on small subunit ribosomal DNA (SSU rDNA) sequences revealed that the family is monophyletic and comprises two subclades (subclades I II) which can be identified by the flexibility of their peristomial lobes and the sculpturing of their necks. Furthermore, we investigate the evolutionary relationships of folliculinids using the six chosen generic features.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00152-z.

Anaerobic Ciliates as a Model Group for Studying Symbioses in Oxygen-depleted Environments

Anaerobiosis has independently evolved in multiple lineages of ciliates, allowing them to colonize a variety of anoxic and oxygen-depleted habitats. Anaerobic ciliates commonly form symbiotic relationships with various prokaryotes, including methanogenic archaea and members of several bacterial groups. The hypothesized functions of these ecto- and endosymbionts include the symbiont utilizing the ciliate's fermentative end-products to increase host's anaerobic metabolic efficiency, or the symbiont directly providing the host with energy by denitrification or photosynthesis. The host, in turn, may protect the symbiont from competition, the environment, and predation. Despite rapid advances in sampling, molecular, and microscopy methods, as well as the associated broadening of the known diversity of anaerobic ciliates, many aspects of these ciliate symbioses, including host-specificity and co-evolution, remain largely unexplored. Nevertheless, with the number of comparative genomic and transcriptomic analyses targeting anaerobic ciliates and their symbionts on the rise, insights into the nature of these symbioses and the evolution of the ciliate transition to obligate anaerobiosis continue to deepen. This review summarizes the current body of knowledge regarding the complex nature of symbioses in anaerobic ciliates, the diversity of these symbionts, their role in the evolution of ciliate anaerobiosis and their significance in ecosystem-level processes.

Taxonomy and SSU rDNA-Based Phylogeny of Two Heterotrich Ciliates (Ciliophora, Heterotrichea) Collected From Subtropical Wetlands of China, Including the Description of a New Species, Linostomella pseudovorticella n. sp

The Heterotrichea Stein, 1859 are a group of ciliated protists (single-celled eukaryotes) that occur in a wide variety of aquatic habitat where they play important roles in the flow of nutrients and energy within the microbial food web. Many species are model organisms for research in cytology and regenerative biology. In the present study, the morphology and phylogeny of two heterotrich ciliates, namely, Linostomella pseudovorticella n. sp. and Peritromus kahli Villeneuve-Brachon, 1940, collected from subtropical wetlands of China, were investigated using morphological and molecular methods. L. pseudovorticella n. sp. differs from its only known congener, Linostomella vorticella Ehrenberg, 1833 Aescht in Foissner et al., 1999, by having more ciliary rows (48-67, mean about 56 vs. 26-51, mean about 42) and its small-subunit (SSU) rDNA sequence, which shows a 15-bp divergence. Although P. kahli has been reported several times in recent decades, its infraciliature has yet to be described. A redescription and improved diagnosis of this species based on a combination of previous and present data are here supplied. Phylogenetic analyses based on SSU rDNA sequences revealed that the genus Linostomella is positioned within Condylostomatidae, and Peritromidae is sister to Climacostomidae with relatively low support, and the family Spirostomidae is the root branch of the class Heterotrichea.

New contributions to the phylogeny of the ciliate class Heterotrichea (Protista, Ciliophora): analyses at family-genus level and new evolutionary hypotheses

Heterotrichous ciliates play an important role in aquatic ecosystem energy flow processes and many are model organisms for research in cytology, regenerative biology, and toxicology. In the present study, we combine both morphological and molecular data to infer phylogenetic relationships at family-genus level and propose new evolutionary hypotheses for the class Heterotrichea. The main results include: (1) 96 new ribosomal DNA sequences from 36 populations, representing eight families and 13 genera, including three poorly annotated genera, Folliculinopsis, Ampullofolliculina and Linostomella; (2) the earliest-branching families are Spirostomidae in single-gene trees and Peritromidae in the concatenated tree, but the family Peritromidae probably represents the basal lineage based on its possession of many "primitive" morphological characters; (3) some findings in molecular trees are not supported by morphological evidence, such as the family Blepharismidae is one of the most recent branches and the relationship between Fabreidae and Folliculinidae is very close; (4) the systematic positions of Condylostomatidae, Climacostomidae, and Gruberiidae remain uncertain based either on morphological or molecular data; and (5) the monophyly of each genus included in the present study is supported by the molecular phylogenetic trees, except for Blepharisma in the SSU rDNA tree and Folliculina in the ITS1-5.8S-ITS2 tree.

A new contribution to the taxonomy and molecular phylogeny of three, well-known freshwater species of the ciliate genus Spirostomum (Protozoa: Ciliophora: Heterotrichea)

Members of the heterotrich genus Spirostomum are commonly found in freshwater or low salinity biotopes. In the present study, three species (S. minus, S. subtilis and S. teres) collected from freshwater habitats in Qingdao, China, are investigated using morphological and molecular methods. Detailed morphometric data are documented and improved diagnosis are supplied based on a combination of previous and present studies. In addition, small subunit ribosomal DNA (SSU rDNA) sequences are obtained from the clonal cultures. Phylogenetic analyses show that all three species are placed in the Spirostomum clade. However, isolates of the morphospecies S. minus are divided into two paraphyletic clades, while ‘populations’ of the nominal species, S. teres, are placed in at least four separate groups in the tree. After comparing morphological and molecular differences in closely related forms available, we hypothesized that S. minus and S. teres might represent species complexes. A key to the identification of the ten valid species of Spirostomum is also supplied.

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.

The Taxonomy and Phylogeny of the Poorly known Heterotrich Ciliate Ampullofolliculina lageniformis Hadži, 1951 (Ciliophora: Heterotrichea)

Ampullofolliculina Hadži, 1951 is a monotypic genus, the only species being A. lageniformis which was first discovered in estuarine habitats in the U.S. and has never been redescribed. In the present study, we investigated the taxonomy and phylogeny of A. lageniformis Hadži, 1951 based on analyses of a population collected from a brackish wetland in Ningbo, China. The main characteristics of this species are as follows: trophont about 450-700 μm long in vivo with two short, rounded peristomial lobes of equal size; lorica flask-shaped, transparent and smooth with a short, wide neck at the base of which two transparent valves are asymmetrically inserted; cortex with brownish to reddish cortical granules and greenish pigment granules; about 80 somatic kineties evenly arranged; moniliform macronucleus with 4-8 ellipsoidal nodules; swarmer dark green, vermiform in shape, about 200-350 μm long in vivo, with about 60 adoral membranelles and 85 somatic kineties, no mouth nor paroral membrane. Phylogenetic analyses inferred from SSU rDNA sequences show that A. lageniformis is closely related to Folliculina and Eufolliculina which nest within a large clade that comprises five families, i.e. Stentoridae, Blepharismidae, Fabreidae, Maristentoridae, and Folliculinidae.

New contributions to Gruberia lanceolata (Gruber, 1884) Kahl, 1932 based on analyses of multiple populations and genes (Ciliophora, Heterotrichea, Gruberiidae)

Gruberia Kahl, 1932 is a species-poor genus comprising only seven named species. Most of these species have not been reinvestigated since the original reports. In the present work, we investigated the taxonomy and phylogeny of Gruberia lanceolata (Gruber, 1884) Kahl, 1932 based on analyses of morphology and multiple gene sequences from four South Korean populations. This species is mainly characterized by a well-developed peristome region, segmented paroral membrane, and moniliform macronucleus. Some morphological features were not stable among the four populations investigated, such as body shape and size, cell color, and the ratio of oral length to body length. However, our molecular analyses of four different genetic markers - three nuclear DNA markers (18S rDNA, ITS1-5.8S-ITS2 region, D1D2 of 28S rDNA) and one mitochondrial (mt) marker (CO1 gene) - indicated that all Korean populations examined were the same species. Based on our present findings and historic works, we propose that G. calkinsi, G. aculeata, and G. beninensis are junior synonyms of G. lanceolata.

Expanded phylogenetic analyses of the class Heterotrichea (Ciliophora, Postciliodesmatophora) using five molecular markers and morphological data

Most studies of the molecular evolution of Heterotrichea have been based solely on the 18S-rDNA gene, which were inconsistent with morphological classification. Because of the limitations of single locus phylogenies and the recurring problem of lack of resolution of deeper nodes found in previous studies, we present hypotheses of the evolution of internal groups of the class Heterotrichea based on multi-loci analyses (18S-rDNA, 28S-rDNA, ITS1-5.8S-ITS2 region, COI and alpha-tubulin) and morphological data. Phylogenetic trees from protein coding gene data are presented for Heterotrichea for the first time. Phylogenetic analyses included Bayesian inference, maximum likelihood, maximum parsimony methods, and optimal trees were statistically compared to alternative topologies from the literature. Additionally, the Bayesian concordance approach (BCA algorithm) was used to assess the concordance factor between topologies obtained from isolated analyses. Because different loci may evolve at different rates, resulting in different gene topologies, we also estimated a species tree for Heterotrichea using the STAR coalescence-based method. The results show that: (1) single gene trees are inconsistent regarding the position of some heterotrichean families; (2) the concatenation of all data in a total-evidence tree improved the resolution of deep nodes among the heterotrichean families and genera; (3) the coalescent-based species tree is consistent with phylogenies based on the 18S-rDNA gene and shows Spirostomidae as the stem group of Heterotrichea; (4) however, the total-evidence tree suggests that the large Heterotrichea cluster is divided into nine lineages in which Peritromidae diverges at the base of the Heterotrichea tree.

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 18S rDNA gene sequence of Blepharisma sinuosum Sawaya, 1940 (Ciliophora: Heterotrichea) from Brazil

The morphology and morphometric data of seven populations of Blepharisma sinuosum from southeastern Brazil were investigated. The description is based on live observations, protargol impregnation, and scanning electron microscopy. Blepharisma sinuosum measures 75-255μm in length and 25-93μm in width and has a spindle-shaped body, pink color, a single contractile vacuole located at the posterior end, 50 adoral membranelles, a conspicuous paroral, 17-35 somatic kineties, a moniliform macronucleus with 2-7 connected nodules, and 3-20 micronuclei. Morphological comparisons with similar species were performed and suggest that B. americanum is the junior synonym of B. sinuosum. The 18S rDNA gene sequence of B. sinuosum was obtained and compared with that of other Blepharisma species. The length and GC content of the obtained sequence is 1652bp and 47.03%, respectively, and has a very high structural similarity (99.9%) with the B. undulans sequence. The validity of the classification of Blepharisma species in morphonuclear subgenera is also discussed.

Small subunit ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1 gene sequences of 21 strains of the parasitic scuticociliate Miamiensis avidus (Ciliophora, Scuticociliatia)

The scuticociliate Miamiensis avidus is a histophagous parasite that causes high mortality in cultured marine fishes. Small subunit ribosomal RNA (SSU rRNA) and mitochondrial cytochrome c oxidase subunit 1 (cox1) genes were analyzed for 21 strains of M. avidus isolated from diseased olive flounder (Paralichthys olivaceus), ridged-eye flounder (Pleuronichthys cornutus), and spotted knifejaw (Oplegnathus fasciatus) in Korea and Japan (collected in 2003-2007). Analysis of SSU rRNA gene sequences (1,759 bp) indicates they are very conserved with less than 0.17% (3 nucleotides) differences suggesting that SSU rRNA are useful to identify M. avidus; however, the cox1 gene (900 bp) has higher variations with intraspecific divergences up to 5.67% (51 nucleotides). A distance tree of cox1 gene sequences based on a neighbor-joining analysis can separate 21 strains into five cox1 types (two heterogeneous clusters and three individual branches). The cox1-type matches with serotype of strains but do not reflect geographical origins, host species, or pathogenicity.

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

Based solely on the localization of the cytostome, Cavalier-Smith (2004) divided the ciliate subphylum Intramacronucleata into three infraphyla: the Spirotrichia, including Armophorea and Spirotrichea; the Rhabdophora, containing exclusively Litostomatea; and the Ventrata, comprising the remaining six intramacronucleate classes. This scheme is supported largely by 18S rRNA phylogenetic analyses presented here, except for the placement of the Armophorea. We argue that this group does not belong to the Spirotrichia but forms a lineage together with the Litostomatea because the molecular sister relationship of the Armophorea and Litostomatea is supported by two morphological and morphogenetic synapomorphies: (i) plate-like arranged postciliary microtubule ribbons, forming a layer right of and between the ciliary rows and (ii) a telokinetal stomatogenesis. Thus, we unite them into a new infraphylum, Lamellicorticata, which replaces Cavalier-Smith's Rhabdophora. Further, our phylogenetic analyses consistently classify the most complex haptorian genus Dileptus basal to all other litostomateans, though morphological investigations suggest dileptids to be highly derived and possibly originating from a spathidiid ancestor. These discrepancies between molecular and morphological classifications have not as yet been investigated in detail. Thus, we propose an evolutionary scenario, explaining both the sister relationship of the Armophorea and Litostomatea, as well as the basal position of the morphologically complex dileptids.

Protocruzia, a highly ambiguous ciliate (Protozoa; Ciliophora): very likely an ancestral form for Heterotrichea, Colpodea or Spirotrichea? With reevaluation of its evolutionary position based on multigene analyses

The ciliate genus Protocruzia belongs to one of the most ambiguous taxa considering its systematic position, possible as a member of the classes Heterotrichea, Spirotrichea or Karyorelictea, which is tentatively placed into Spirotrichea in Lynn's 2008 system. To test these hypotheses, multigene trees (Bayesian inference, evolutionary distance, maximum parsimony, and maximum likelihood) were constructed using the small subunit rRNA (SSU rRNA) gene, internal transcribed spacer 2 (ITS2) and a protein coding gene (histone H4). All analyses agree that: (1) four morphotypes of Protocruzia from different geographical origins group together and form a monophyletic clade, which cannot be assigned to any of the eleven described ciliate classes; (2) it is invariably positioned on an isolated branch separated from the class Spirotrichea suggesting that this clade should be clearly removed from Spirotrichea; (3) this leads us to hypothesize that this taxon may indeed represent a lineage on a class rank. Based on the fact that it is, both morphologically and in molecular features, closely related to heterotrichs, Colpodea and Oligohymenophorea, Protocruziida might be an ancestral form for the subphylum Intramacronucleata in the evolutionary line from the class Heterotrichea (subphylum Postciliodesmatophora) to higher taxa.