Delimitation of five astome ciliate species isolated from the digestive tube of three ecologically different groups of lumbricid earthworms, using the internal transcribed spacer region and the hypervariable D1/D2 region of the 28S rRNA gene

Rediscovery and morpho-molecular characterization of three astome ciliates, with new insights into eco-evolutionary associations of astomes with their annelid hosts

Astome ciliates live in the digestive tract of a broad spectrum of marine, freshwater, and terricolous annelids. In aquatic lumbriculid and criodrilid oligochaetes collected in Central Europe, we rediscovered three insufficiently known astomes: Hoplitophrya secans, Mesnilella clavata, and Buchneriella criodrili. Their morphology was studied using in vivo observation, protargol, and dry silver nitrate impregnation. Multiple nuclear and mitochondrial molecular markers were used to determine their phylogenetic positions and reconstruct their evolutionary history. According to our phylogenetic analyses: (1) mouthless ciliates isolated from annelids form a robustly supported monophylum within the class Oligohymenophorea, (2) the progenitor of astomes invaded the digestive tract of marine polychaetes during the Paleozoic era, (3) lumbricid earthworms likely served as a source of astomes for criodrilid, almid, and megascolecid earthworms, (4) the ancestral host of the earthworm-dwelling astome clade led an endogeic lifestyle, and (5) there were multiple independent transfers of astomes from endogeic to epigeic and anecic earthworms. These findings support previous views of the annelid phylogeny, suggesting that astomes reside and evolve in tandem with annelids for several hundred million years.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00275-5.

Molecular identification and studies on genetic diversity and structure-related GC heterogeneity of Spatholobus Suberectus based on ITS2

To determine the role of internal transcribed spacer 2 (ITS2) in the identification of Spatholobus suberectus and explore the genetic diversity of S. suberectus. A total of 292 ITS2s from S. suberectus and 17 other plant species were analysed. S. suberectus was clustered separately in the phylogenetic tree. The genetic distance between species was greater than that within S. suberectus. Synonymous substitution rate (Ks) analysis revealed that ITS2 diverged the most recently within S. suberectus (Ks = 0.0022). These findings suggested that ITS2 is suitable for the identification of S. suberectus. The ITS2s were divided into 8 haplotypes and 4 evolutionary branches on the basis of secondary structure, indicating that there was variation within S. suberectus. Evolutionary analysis revealed that the GC content of paired regions (pGC) was greater than that of unpaired regions (upGC), and the pGC showed a decreasing trend, whereas the upGC remained unchanged. Single-base mutation was the main cause of base pair substitution. In both the initial state and the equilibrium state, the substitution rate of GC was higher than that of AU. The increase in the GC content was partly attributed to GC-biased gene conversion (gBGC). High GC content reflected the high recombination and mutation rates of ITS2, which is the basis for species identification and genetic diversity. We characterized the sequence and structural characteristics of S. suberectus ITS2 in detail, providing a reference and basis for the identification of S. suberectus and its products, as well as the protection and utilization of wild resources.

Deciphering phylogenetic relationships of and delimiting species boundaries within the controversial ciliate genus Conchophthirus using an integrative morpho-evo approach

The phylum Ciliophora (ciliates) comprises about 2600 symbiotic and over 5500 free-living species. The inclusion of symbiotic ciliates in phylogenetic analyses often challenges traditional classification frameworks due to their morphological adaptions to the symbiotic lifestyle. Conchophthirus is such a controversial obligate endocommensal genus whose affinities to other symbiotic and free-living scuticociliates are still poorly understood. Using uni- and multivariate morphometrics as well as 2D-based molecular and phylogenetic analyses, we attempted to test for the monophyly of Conchophthirus, study the boundaries of Conchophthirus species isolated from various bivalves at mesoscale, and reveal the phylogenetic relationships of Conchophthirus to other scuticociliates. Multidimensional analyses of morphometric and cell geometric data generated the same homogenous clusters, as did phylogenetic analyses based on 144 new sequences of two mitochondrial and five nuclear molecular markers. Conchophthirus is not closely related to 'core' scuticociliates represented by the orders Pleuronematida and Philasterida, as assumed in the past using morphological data. Nuclear and mitochondrial markers consistently showed the free-living Dexiotricha and the mouthless endosymbiotic Haptophrya to be the nearest relatives of Conchophthirus. These three highly morphologically and ecologically dissimilar genera represent an orphan clade from the early radiation of scuticociliates in molecular phylogenies.

First molecular evidence of hybridization in endosymbiotic ciliates (Protista, Ciliophora)

Hybridization is an important evolutionary process that can fuel diversification via formation of hybrid species or can lead to fusion of previously separated lineages by forming highly diverse species complexes. We provide here the first molecular evidence of hybridization in wild populations of ciliates, a highly diverse group of free-living and symbiotic eukaryotic microbes. The impact of hybridization was studied on the model of Plagiotoma, an obligate endosymbiont of the digestive tube of earthworms, using split decomposition analyses and species networks, 2D modeling of the nuclear rRNA molecules and compensatory base change analyses as well as multidimensional morphometrics. Gene flow slowed down and eventually hampered the diversification of Lumbricus-dwelling plagiotomids, which collapsed into a single highly variable biological entity, the P. lumbrici complex. Disruption of the species boundaries was suggested also by the continuum of morphological variability in the phenotypic space. On the other hand, hybridization conspicuously increased diversity in the nuclear rDNA cistron and somewhat weakened the host structural specificity of the P. lumbrici complex, whose members colonize a variety of phylogenetically closely related anecic and epigeic earthworms. By contrast, another recorded species, P. aporrectodeae sp. n., showed no signs of introgression, no variability in the rDNA cistron, and very high host specificity. These contrasting eco-evolutionary patterns indicate that hybridization might decrease the alpha-diversity by dissolving species boundaries, weaken the structural host specificity by broadening ecological amplitudes, and increase the nuclear rDNA variability by overcoming concerted evolution within the P. lumbrici species complex.

Characterization of a Pseudokeronopsis Strain (Ciliophora, Urostylida) and Its Bacterial Endosymbiont “Candidatus Trichorickettsia” (Alphaproteobacteria, Rickettsiales)

Symbiotic associations between bacteria and ciliate protists are rather common. In particular, several cases were reported involving bacteria of the alphaproteobacterial lineage Rickettsiales, but the diversity, features, and interactions in these associations are still poorly understood. In this work, we characterized a novel ciliate protist strain originating from Brazil and its associated Rickettsiales endosymbiont by means of live and ultrastructural observations, as well as molecular phylogeny. Though with few morphological peculiarities, the ciliate was found to be phylogenetically affiliated with Pseudokeronopsis erythrina, a euryhaline species, which is consistent with its origin from a lagoon with significant spatial and seasonal salinity variations. The bacterial symbiont was assigned to “Candidatus Trichorickettsia mobilis subsp. hyperinfectiva”, being the first documented case of a Rickettsiales associated with urostylid ciliates. It resided in the host cytoplasm and bore flagella, similarly to many, but not all, conspecifics in other host species. These findings highlight the ability of “Candidatus Trichorickettsia” to infect multiple distinct host species and underline the importance of further studies on this system, in particular on flagella and their regulation, from a functional and also an evolutionary perspective, considering the phylogenetic proximity with the well-studied and non-flagellated Rickettsia.

Nuclear and Mitochondrial SSU rRNA Genes Reveal Hidden Diversity of Haptophrya Endosymbionts in Freshwater Planarians and Challenge Their Traditional Classification in Astomatia

Like many other aquatic animals, freshwater planarians have also become partners of symbiotic ciliates from the class Oligohymenophorea. In the present study, we explored the hidden diversity and addressed the questionable systematic position of mouthless obligatory gut endosymbionts of freshwater planarians, using the nuclear and mitochondrial SSU rRNA genes. Although all isolated ciliates morphologically corresponded to a single species, molecular analyses suggested the existence of three genetically distinct entities: Haptophrya planariarum, Haptophrya dugesiarum nov. spec., and Haptophrya schmidtearum nov. spec. The two former species share the same planarian host, which indicates a speciation model involving one duplication event without host switching. Such a diversification pattern was recognized also in astome ciliates inhabiting megascolecid and glossoscolecid earthworms. The present multi-gene phylogenies along with the secondary structure of the mitochondrial 16S rRNA molecule, however, challenge the traditional classification of Haptophrya within the subclass Astomatia. Haptophrya very likely evolved from an orphan scuticociliate lineage by the loss of oral apparatus and by the transformation of the thigmotactic field into an adhesive sucker. Since astomy evolved multiple times independently within the Oligohymenophorea, the loss of cell mouth cannot be used as a sole argument for the assignment of Haptophrya to the Astomatia anymore.

DNA barcoding and coalescent-based delimitation of endosymbiotic clevelandellid ciliates (Ciliophora: Clevelandellida): a shift to molecular taxonomy in the inventory of ciliate diversity in panesthiine cockroaches

Phylogenetically distinct lineages may be hidden behind identical or highly similar morphologies. The phenomenon of morphological crypticity has been recently detected in symbiotic ciliates of the family Clevelandellidae, as multivariate and Fourier shape analyses failed to distinguish genetically distinct taxa. To address the question of species boundaries, the phylogenetic information contained in the rDNA cistron of clevelandellid ciliates, which had been isolated from the digestive tract of blaberid cockroaches, was studied using a multifaceted statistical approach. Multigene phylogenies revealed that the genus Clevelandella is paraphyletic containing members of the genus Paraclevelandia. To resolve the paraphyly of Clevelandella, two new genera, Anteclevelandella gen. nov. and Rhynchoclevelandella gen. nov., are proposed based on morphological synapomorphies and shared molecular characters. Multigene analyses and Bayesian species delimitation supported the existence of 13 distinct species within the family Clevelandellidae, eight of which represent new taxa. Moreover, two new Nyctotherus species were recognized within the clade that is sister to the Clevelandellidae. According to the present distance and network analyses, the first two domains of the 28S rRNA gene showed much higher power for species discrimination than the 18S rRNA gene and ITS region. Therefore, the former molecular marker was proposed to be a suitable group-specific barcode for the family Clevelandellidae.

Multiple independent losses of cell mouth in phylogenetically distant endosymbiotic lineages of oligohymenophorean ciliates: A lesson from Clausilocola

The cell mouth is a property of the vast majority of free-living and endosymbiotic/epibiotic ciliates of the class Oligohymenophorea. Cytostome, however, naturally absents in the whole endosymbiotic subclass Astomatia and was naturally or experimentally lost in a few members of the subclass Hymenostomatia. This poses a question of how homoplastic might be the lack of oral structures in the oligohymenophorean evolution. To address this question, we used two mitochondrial genes, five nuclear markers, and detailed morphological data from an enigmatic mouthless ciliate, Clausilocola apostropha, which we re-discovered after more than half of a century. According to the present phylogenetic analyses, astomy evolved at least three times independently and in different time frames of the oligohymenophorean phylogeny, ranging from the Paleozoic to the Cenozoic period. Mouthless endosymbionts inhabiting mollusks (represented by Clausilocola), planarians (Haptophrya), and annelids ('core' astomes) never clustered together. Haptophrya grouped with the scuticociliate genus Conchophthirus, 'core' astomes were placed in a sister position to the scuticociliate orders Philasterida and Pleuronematida, and Clausilocola was robustly nested within the hymenostome family Tetrahymenidae. The tetrahymenid origin of Clausilocola is further corroborated by the existence of mouthless Tetrahymena mutants and the huge phenotypic plasticity in the cytostome size in tetrahymenids.

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.

Cryptic host-driven speciation of mobilid ciliates epibiotic on freshwater planarians

Mobilids are among the most taxonomically diverse but morphologically uniform groups of epibiotic ciliates. They attach to their hosts by means of an adhesive disc as harmless commensals such as Urceolaria, or as parasites causing significant economic loss such as some Trichodina species. We investigated the diversity, species boundaries, and phylogenetic relationships of mobilids associated with freshwater planarians, using 114 new sequences of two mitochondrial (16S rRNA gene and cytochrome c oxidase gene) and five nuclear (18S rRNA gene, ITS1-5.8S-ITS2 region, D1/D2 domains of 28S rRNA gene) markers. Although the morphological disparity of the isolated trichodinids and urceolariids was low, Bayesian coalescent analyses revealed the existence of five distinct evolutionary lineages/species given the seven molecular markers. The occurrence of mobilids perfectly correlated with their planarian hosts: Trichodina steinii and two Urceolaria mitra-like taxa were associated exclusively with the planarian Dugesia gonocephala, Trichodina polycelis sp. n. with the planarian Polycelis felina, and Trichodina schmidtea sp. n. with the planarian Schmidtea polychroa. Host organisms thus very likely constitute sharply isolated niches that might permit speciation of their epibiotic ciliates, even though no distinct morphological features appear to be recognizable among ciliates originating from different hosts.

Diversity and Eco-Evolutionary Associations of Endosymbiotic Astome Ciliates With Their Lumbricid Earthworm Hosts

Coevolution of endosymbionts with their hosts plays an important role in the processes of speciation and is among the most fascinating topics in evolutionary biology. Astome ciliates represent an interesting model for coevolutionary studies because they are so tightly associated with their host organisms that they completely lost the cell oral apparatus. In the present study, we used five nuclear markers (18S rRNA gene, ITS1-5.8S-ITS2 region, and 28S rRNA gene) and two mitochondrial genes (16S rRNA gene and cytochrome c oxidase subunit I) to explore the diversity of astomes inhabiting the digestive tract of lumbricid earthworms at temperate latitudes in Central Europe and to cast more light on their host specificity and coevolution events that shaped their diversification. The present coevolutionary and phylogenetic interaction-adjusted similarity analyses suggested that almost every host switch leads to speciation and firm association with the new host. Nevertheless, the suggested high structural host specificity of astomes needs to be tested with increased earthworm sampling, as only 52 out of 735 lumbricid earthworms (7.07%) were inhabited by ciliates. On the other hand, the diversification of astomes associated with megascolecid and glossoscolecid earthworms might have been driven by duplication events without host switching.

Re-discovery and novel contributions to morphology and multigene phylogeny of Myxophyllum steenstrupi (Ciliophora: Pleuronematida), an obligate symbiont of terrestrial pulmonates

Myxophyllum steenstrupi is a symbiotic ciliate living in the body slime and mantle cavity of terrestrial pulmonates (Gastropoda: Pulmonata). In the present study, M. steenstrupi was re-discovered after almost 30 years and characterized using an integrative morpho-molecular approach for the first time. Myxophyllum is distinguished by a broadly ovate, about 140 × 115 μm-sized body, a nuclear apparatus typically composed of seven macronuclear nodules and a single micronucleus, a central contractile vacuole, a shallow oral cavity situated in the posterior body region and dense somatic ciliature with extensive thigmotactic field. According to the present phylogenetic analyses of two mitochondrial and five nuclear markers, M. steenstrupi is classified in the predominantly free-living order Pleuronematida (Oligohymenophorea: Scuticociliatia). This order also encompasses other taxa isolated from molluscs and traditionally classified along with Myxophyllum in the order Thigmotrichida. The proper classifications of Myxophyllum was hampered by the dramatic remodelling of its oral apparatus (reduction of the paroral membrane and adoral organelles, formation of vestibular kineties), a transformation that was likely induced by its firm association with terrestrial gastropods. The present study also documents that various ciliate lineages independently became commensals or parasites of various aquatic and terrestrial molluscs.