Evolutionary Origin and Host Range of Plagiotoma lumbrici (Ciliophora, Hypotrichia), an Obligate Gut Symbiont of Lumbricid Earthworms

Symbionts of Ciliates and Ciliates as Symbionts

Endosymbiotic relationships between ciliates and others are critical for their ecological roles, physiological adaptations, and evolutionary implications. These can be obligate and facultative. Symbionts often provide essential nutrients, contribute to the ciliate's metabolism, aid in digestion, and offer protection against predators or environmental stressors. In turn, ciliates provide a protected environment and resources for their symbionts, facilitating their survival and proliferation. Ultrastructural and full-cycle rRNA approaches are utilized to identify these endosymbionts. Fluorescence in situ hybridization using "species- and group-specific probes" which are complementary to the genetic material (DNA or RNA) of a particular species or group of interest represent convenient tools for their detection directly in the environment. A systematic survey of these endosymbionts has been conducted using both traditional and metagenomic approaches. Ciliophora and other protists have a wide range of prokaryotic symbionts, which may contain potentially pathogenic bacteria. Ciliates can establish symbiotic relationships with a variety of hosts also, ranging from protists to metazoans. Understanding ciliate symbiosis can provide useful insights into the complex relationships that drive microbial communities and ecosystems in general.

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.

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.

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.

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.