Bozasella gracilis n. sp. (Ciliophora, Entodiniomorphida) from Asian elephant and phylogenetic analysis of entodiniomorphids and vestibuliferids

Morphology and phylogeny of Pararaabena dentata Wolska, 1968 and further insights into the molecular evolution of trichostome ciliates (Ciliophora, Litostomatea)

The morphology and phylogenetic position of a trichostome ciliate, Pararaabena dentata, isolated from the intestine of an Asian elephant (Elaphas maximus) in Gaziantep Zoo, Turkey, were studied using pyridinated silver carbonate impregnation, scanning electron microscopy, and the 18S rRNA gene. Pararaabena dentata clustered together with Raabena bella and both taxa were phylogenetically not related to members of the family Blepharocorythidae, as expected in the past. Phylogenetic trees indicated that amphibian intestinal ciliates represented by Balantidium grimi, B. duodeni, and B. entozoon are basal to all other trichostome ciliates, causing the family Balantidiidae to be polyphyletic. The molecular evolution of the subclass Trichostomatia is thoroughly discussed.

Phylogenomics corroborates morphology: New discussions on the systematics of Trichostomatia (Ciliophora, Litostomatea)

The subclass Trichostomatia (Ciliophora, Litostomatea) constitutes a well-supported monophyletic group, which includes ciliates exclusively found as symbionts of vertebrates, primarily herbivorous mammals. Recent molecular analyses reinforce the subclass monophyly, though almost all orders, suborders, families, and genera are found to be non-monophyletic. Here, we reconstructed the evolutionary history of the subclass Trichostomatia using a phylogenomic approach and discussed some systematic inconsistencies. We propose a new Ophryoscolecidae genus, Dagostonium, to include Diplodinium polygonale. Monoposthium cynodontum is transferred to the genus Cycloposthium.

Ciliates from the faeces of the free-ranging dromedary from Oman: Morphology and molecular phylogeny

Ciliates Infundibulorium cameli from the faeces of the free-ranging dromedary from Oman were studied using a set of methods of the light and immunofluorescence microscopy and molecular phylogeny. With the use of molecular genetic methods, it was confirmed that the cysts found in the samples simultaneously with trophozoites actually belong to the species I. cameli. Tubulin cytoskeleton organization of trophozoites and cysts of this species were described for the first time. A striking morphological similarity between species I. cameli and Buxtonella sulcata was demonstrated, including the organization of ciliature. Different isolates of I. cameli and B. sulcata formed a common clade on the phylogenetic tree. The level of evolutionary divergence between the 18 S rRNA sequences of I. cameli, B. sulcata and species closest to them according to the results of molecular phylogenetic analysis was estimated. It was demonstrated that the divergence between I. cameli and B. sulcata is extremely low compared to members of other genera included in the analysis. Taxonomic position of I. cameli and B. sulcata was discussed in according to the data of comparative morphology and molecular phylogeny.

Question of agent of camel balantidiosis solved: Molecular identity, taxonomic solution and epidemiological considerations

Domestic camels (Camelus bactrianus, the Bactrian camel; and Camelus dromedarius, the dromedary) are pseudo-ruminant herbivores kept as livestock in rural, inhospitable regions (cold deserts and dry steppes of Asia, arid to semi-arid regions of Africa, western and central Asia). Their close contact with humans makes them a potential reservoir for zoonotic parasite infections, as has been suggested for human balantidiasis. However, there is confusion about the ciliate species that infects camels: Infundibulorium cameli was originally described in dromedaries, but this name has almost never been used and most authors identified their findings as Balantioides coli and, to a lesser extent, Buxtonella sulcata, a cattle ciliate. To clarify the taxonomic status of the parasite and the corresponding zoonotic significance for camels, we performed morphological characterization of cysts and genetic analysis (SSU-rDNA and ITS markers) of B. coli-like isolates from Bactrian camels from Bulgaria and from dromedaries from Spain and the United Arab Emirates. Our results indicate that the camel ciliate is not B. coli, nor is it B. sulcata, but is a different species that should be placed in the same genus as the latter. Thus, camels are not a reservoir for human balantidiasis. Although the correct genus name would be Infundibulorium according to the principle of priority, this would lead to confusion since this name has almost fallen into disuse since its initial description, but Buxtonella is almost universally used by researchers and veterinarians for the cattle ciliate. We therefore propose to apply the reversal of precedence and use Buxtonella as the valid genus name. Consequently, we propose Buxtonella cameli n.comb. as the name for the camel ciliate.

Ciliates from the intestine of zoo-kept black rhinoceros, with immunofluorescence microscopic and molecular phylogenetic investigation of Rhinozeta rhinozeta (Litostomatea)

The study of endobiotic ciliates from the intestines of various zoo mammals is important for revealing the influence of various factors on endobiont communities. In this paper we describe the species diversity of endobiotic ciliates from the faeces of the eastern black rhinoceros Diceros bicornis michaeli (male and two females, mother and daughter) kept in the zoo. Seven species of the ciliates were found, among them Rhinozeta rhinozeta, R. triciliata and Prototapirella clypeata were observed in the rhinos only. The other two, Monoposthium sp. and Triplumaria sp., according to their morphology should have been identified as new ciliate species. Successful transmission of the endobionts from parents to the young rhino in the zoo was demonstrated. R. rhinozeta was investigated with the using of the methods of the light and immunofluorescence microscopy and molecular phylogeny. The composition and phylogeny of the family Cycloposthiidae were discussed.

New Finds on the Systematics of Cycloposthiid Ciliates (Ciliophora: Entodiniomorphida: Cycloposthiidae) Based on New 18S-rDNA Sequences from a Brazilian Capybara

The family Cycloposthiidae (Entodiniomorphida) comprises ciliated protists that are symbionts of the gastrointestinal tract of several herbivore mammals, such as rodents, elephants, equids, primates, hippopotamus, marsupials, rhinoceros and tapir, where they contribute to the digestion of their host's plant-based diet. Despite the significance of these ciliates to the evolution of their hosts, many characters used in the taxonomy of the group are homoplastic and most of the valid species do not have molecular data available. For these reasons the systematics of this family is poorly understood. Here, we sequenced the 18S-rDNA of ten cycloposthiids, including nine Cycloposthium spp. and Monoposthium cynodontum, all of them isolated from the cecum of a Brazilian capybara. Our phylogenetic analyses indicate that the family Cycloposthiidae might be polyphyletic, while M. cynodontum and Cycloposthium spp. constitute a single monophyletic group. Given the great morphological and molecular similarities between members of M. cynodontum and Cycloposthium ciliates, it is possible that this species, although it has been described in the genus Monoposthium, is actually a Cycloposthium ciliate.

Balantioides coli

Balantioides coli (=Balantidium coli) is the only ciliate that parasitizes humans. Pigs are the main reservoir. Other species, as camels, cattle, donkey, sheep and goat have been also proposed as reservoirs for human infections. The parasite has a direct life cycle, being transmitted by the faecal-oral route. This type of cycle and the large number of host species imply an important potential for zoonotic transmission of the parasite. Infections are most commonly found in tropical and temperate regions, with prevalence up to 100% in pigs; high prevalence values have been also recorded in some non-human primates and camels. In humans, prevalence is usually under 10% in the population at risk. The main epidemiological factors involved in the transmission of this parasite include close contact with pigs, lack of basic sanitation infrastructures (water supply, wastewater disposal) and hygiene. Individual health status, intestinal microbiota and diet are also important for the onset of the infection. Outbreaks caused by this parasite are rare; those reported to date were related to poor hygienic conditions or to catastrophic natural disasters. Balantioides coli infections can be asymptomatic and symptomatic, which can be chronic (with intermittent diarrhoea), or acute (a dysenteric form which can be life-threatening). Efective treatments include tetracycline, iodoquinol and 5-nitroimidazole compounds (metronidazole, secnidazole). The main effective individual preventive measure is the use of disinfected water for drinking and other uses. Adequate water supply infrastructures, proper disposal of wastewater and animal faeces, and regular monitoring programs on farms will help limit transmission.

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

Background

Various ecological groups of earthworms very likely constitute sharply isolated niches that might permit speciation of their symbiotic ciliates, even though no distinct morphological features appear to be recognizable among ciliates originating from different host groups. The nuclear highly variable ITS1–5.8S-ITS2 region and the hypervariable D1/D2 region of the 28S rRNA gene have proven to be useful tools for the delimitation of species boundaries in closely related free-living ciliate taxa. In the present study, the power of these molecular markers as well as of the secondary structure of the ITS2 molecule were tested for the first time in order to discriminate the species of endosymbiotic ciliates that were isolated from the gastrointestinal tract of three ecologically different groups of lumbricid earthworms.

Results

Nineteen new ITS1–5.8S-ITS2 region and D1/D2-28S rRNA gene sequences were obtained from five astome species (Anoplophrya lumbrici, A. vulgaris, Metaradiophrya lumbrici, M. varians, and Subanoplophrya nodulata comb. n.), which were living in the digestive tube of three ecological groups of earthworms. Phylogenetic analyses of the rRNA locus and secondary structure analyses of the ITS2 molecule robustly resolved their phylogenetic relationships and supported the distinctness of all five species, although previous multivariate morphometric analyses were not able to separate congeners in the genera Anoplophrya and Metaradiophrya. The occurrence of all five taxa, as delimited by molecular analyses, was perfectly correlated with the ecological groups of their host earthworms.

Conclusions

The present study indicates that morphology-based taxonomy of astome ciliates needs to be tested in the light of molecular and ecological data as well. The use of morphological identification alone is likely to miss species that are well delimited based on molecular markers and ecological traits and can lead to the underestimation of diversity and overestimation of host range. An integrative approach along with distinctly increased taxon sampling would be helpful to assess the consistency of the eco-evolutionary trend in astome ciliates.

The structure of microbial populations in Nelore GIT reveals inter-dependency of methanogens in feces and rumen

Background

The success of different species of ruminants in the colonization of a diverse range of environments is due to their ability to digest and absorb nutrients from cellulose, a complex polysaccharide found in leaves and grass. Ruminants rely on a complex and diverse microbial community, or microbiota, in a unique compartment known as the rumen to break down this polysaccharide. Changes in microbial populations of the rumen can affect the host’s development, health, and productivity. However, accessing the rumen is stressful for the animal. Therefore, the development and use of alternative sampling methods are needed if this technique is to be routinely used in cattle breeding. To this end, we tested if the fecal microbiome could be used as a proxy for the rumen microbiome due to its accessibility. We investigated the taxonomic composition, diversity and inter-relations of two different GIT compartments, rumen and feces, of 26 Nelore (Bos indicus) bulls, using Next Generation Sequencing (NGS) metabarcoding of bacteria, archaea and ciliate protozoa.

Results

We identified 4265 Amplicon Sequence Variants (ASVs) from bacteria, 571 from archaea, and 107 from protozoa, of which 143 (96 bacteria and 47 archaea) were found common between both microbiomes. The most prominent bacterial phyla identified were Bacteroidetes (41.48%) and Firmicutes (56.86%) in the ruminal and fecal microbiomes, respectively, with Prevotella and Ruminococcaceae UCG-005 the most relatively abundant genera identified in each microbiome. The most abundant archaeal phylum identified was Euryarchaeota, of which Methanobrevibacter gottschalkii, a methanogen, was the prevalent archaeal species identified in both microbiomes. Protozoa were found exclusively identified in the rumen with Bozasella/Triplumaria being the most frequent genus identified. Co-occurrence among ruminal and fecal ASVs reinforces the relationship of microorganisms within a biological niche. Furthermore, the co-occurrence of shared archaeal ASVs between microbiomes indicates a dependency of the predominant fecal methanogen population on the rumen population.

Conclusions

Co-occurring microorganisms were identified within the rumen and fecal microbiomes, which revealed a strong association and inter-dependency between bacterial, archaeal and protozoan populations of the same microbiome. The archaeal ASVs identified as co-occurring between GIT compartments corresponded to the methanogenic genera Methanobrevibacter and Methanosphaera and represented 26.34% of the overall archaeal sequencesdiversity in the rumen and 42.73% in feces. Considering that these archaeal ASVs corresponded to a significant part of the overall diversity of both microbiomes, which is much higher if one includes the interactions of these co-occurring with other rumen archaea ASVs, we suggest that fecal methanogens could be used as a proxy of ruminal methanogens.

Trichostomatid Ciliates (Alveolata, Ciliophora, Trichostomatia) Systematics and Diversity: Past, Present, and Future

The gastrointestinal tracts of most herbivorous mammals are colonized by symbiotic ciliates of the subclass Trichostomatia, which form a well-supported monophyletic group, currently composed by ∼1,000 species, 129 genera, and 21 families, distributed into three orders, Entodiniomorphida, Macropodiniida, and Vestibuliferida. In recent years, trichostomatid ciliates have been playing a part in many relevant functional studies, such as those focusing in host feeding efficiency optimization and those investigating their role in the gastrointestinal methanogenesis, as many trichostomatids are known to establish endosymbiotic associations with methanogenic Archaea. However, the systematics of trichostomatids presents many inconsistencies. Here, we stress the importance of more taxonomic works, to improve classification schemes of this group of organisms, preparing the ground to proper development of such relevant applied works. We will present a historical review of the systematics of the subclass Trichostomatia highlighting taxonomic problems and inconsistencies. Further on, we will discuss possible solutions to these issues and propose future directions to leverage our comprehension about taxonomy and evolution of these symbiotic microeukaryotes.

Helmet-shaped Body of Entodiniomorphid Ciliates (Ciliophora, Entodiniomorphida), a Synapomorphy or a Homoplasy?

Triadinium was created to include Triadinium caudatum. Further, four other species were included, T. minimum, T. galea, T. elongatum, and T. magnum, all sharing a characteristic helmet-shaped body. Wolska and Grain argued that the inclusion of T. minimum and T. galea into Triadinium was done based on superficial morphological aspects, and established two new genera to accommodate these species: Circodinium and Gassovskiella. Although the phylogenetic relationships within Entodiniomorphida have been investigated by multiple authors, none of them discussed the evolutionary relationship of helmet-shaped entodiniomorphids. We performed molecular phylogenetics and revisited old literature digging for morphological data to explain our results. According to our analyses, the helmet-shaped body is homoplastic and may have evolved from at least three different entodiniomorphid ancestors. Circodinium minimum is phylogenetically related to members of Blepharocorythidae, T. caudatum emerged within Spirodiniidae and G. galea within Polydiniellidae. This phylogenetic hypothesis is partially supported by information on infraciliature and ultrastructure of C. minimum and T. caudatum. However, such morphological information is not available for polydiniellids. In order to shed some light into the evolution of the helmet-shaped ciliates, future works should focus to collect information on the infraciliature and the ultrastructure of Polydiniella mysorea and of other Triadinium species.

Living morphology and molecular phylogeny of oligohymenophorean ciliates associated with freshwater turbellarians

Three freshwater turbellarian species (Dugesia gonocephala, Girardia tigrina, and Polycelis felina), belonging to the order Tricladida, were examined for the presence of ciliates. Living morphology and phylogenetic position of the isolated ciliates were studied using light microscopy and molecular phylogenetic methods. Three ciliate species, all from the highly diverse class Oligohymenophorea, were detected: Haptophrya planariarum from the subclass Astomatia, Urceolaria mitra from the subclass Peritrichia, and Tetrahymena sp. from the subclass Hymenostomatia. Each of these ciliates is specialized for different parts of the turbellarian bodies: H. planariarum lives in the pharynx and rami of the intestine, U. mitra colonizes the body surface, and Tetrahymena sp. attacks open wounds and feeds on the mesenchyme. Astomes and peritrichs isolated from turbellarians are placed deeper in 18S rRNA gene phylogenies than their relatives isolated from annelids and mollusks. On the other hand, Tetrahymena sp. isolated from turbellarians is classified comparatively deeply within the family Tetrahymenidae, suggesting that the phylogeny of tetrahymenids does not correlate with that of their obligate/facultative host groups. Nevertheless, the reconstruction of ancestral traits corroborated the hypothesis that histophagy was already a life history trait of the progenitor of the subclass Hymenostomatia to which Tetrahymena belongs.

Evolutionary Associations of Endosymbiotic Ciliates Shed Light on the Timing of the Marsupial-Placental Split

Trichostome ciliates are among the most conspicuous protists in the gastrointestinal tract of a large variety of vertebrates. However, little is still known about phylogeny of the trichostome/vertebrate symbiotic systems, evolutionary correlations between trichostome extrinsic traits, and character-dependent diversification of trichostomes. These issues were investigated here, using the relaxed molecular clock technique along with stochastic mapping of character evolution, and binary-state speciation and extinction models. Clock analyses revealed that trichostomes colonized the vertebrate gastrointestinal tract ∼135 Ma, that is, near the paleontological minimum for the split of therian mammals into marsupials and placentals. According to stochastic mapping, the last common ancestor of trichostomes most likely invaded the hindgut of a mammal. Although multiple shifts to fish/amphibian or avian hosts and to the foregut compartments took place during the trichostome phylogeny, only transition to the foregut was recognized as a key innovation responsible for the explosive radiation of ophryoscolecid trichostomes after the Cretaceous/Tertiary boundary, when ungulates began their diversification. Since crown radiations of main trichostome lineages follow those of their mammalian hosts and are in agreement with their historic dispersal routes, the present time-calibrated phylogeny might help to elucidate controversies in the geological and molecular timing of the split between marsupials and placental mammals.

Balantidium grimi n. sp. (Ciliophora, Litostomatea), a new species inhabiting the rectum of the frog Quasipaa spinosa from Lishui, China

Balantidium grimi n. sp. is described from the rectum of the frog Quasipaa spinosa (Amphibia, Dicroglossidae) from Lishui, Zhejiang Province, China. The new species is described by both light microscopy (LM) and scanning electron microscopy (SEM), and a molecular phylogenetic analysis is also presented. This species has unique morphological features in that the body shape is somewhat flattened and the vestibulum is “V”-shaped, occupying nearly 3/8 to 4/7 of the body length. Only one contractile vacuole, situated at the posterior body, was observed. The phylogenetic analysis based on SSU-rDNA indicates that B. grimi groups together with B. duodeni and B. entozoon. In addition, the genus Balantidium is clearly polyphyletic.

Phylogenetic Analyses Support Validity of Genus Eodinium (Ciliophora, Entodiniomorphida, Ophryoscolecidae)

The validity of genus Eodinium has been historically disputed due to morphological similarities with Diplodinium (absence of skeletal plates as well as adoral and dorsal ciliary zones at the same body level). To address this issue, the 18S rDNA of four Eodinium posterovesiculatum morphotypes and four Diplodinium anisacanthum morphotypes were sequenced and phylogenetically analyzed. The different inference methods suggest the existence of a last common ancestor of Eodinium and Ostracodinium that is not shared with Diplodinium, strongly supporting the validity of genus Eodinium. Since skeletal plates are present in all members of genus Ostracodinium, the most parsimonious is a secondary loss of skeletal plates in E. posterovesiculatum. This work represents a breakthrough in the taxonomy and phylogeny of the family Ophryoscolecidae indicating that the skeletal plates may not reflect evolutionary divergence within this group of ciliates as traditionally proposed.

Phylogeny of intestinal ciliates, including Charonina ventriculi, and comparison of microscopy and 18S rRNA gene pyrosequencing for rumen ciliate community structure analysis

The development of high-throughput methods, such as the construction of 18S rRNA gene clone or pyrosequencing libraries, has allowed evaluation of ciliate community composition in hundreds of samples from the rumen and other intestinal habitats. However, several genera of mammalian intestinal ciliates have been described based only on morphological features and, to date, have not been identified using molecular methods. Here, we isolated single cells of one of the smallest but widely distributed intestinal ciliates, Charonina ventriculi, and sequenced its 18S rRNA gene. We verified the sequence in a full-cycle rRNA approach using fluorescence in situ hybridization and thereby assigned an 18S rRNA gene sequence to this species previously known only by its morphology. Based on its full-length 18S rRNA gene sequence, Charonina ventriculi was positioned within the phylogeny of intestinal ciliates in the subclass Trichostomatia. The taxonomic framework derived from this phylogeny was used for taxonomic assignment of trichostome ciliate 18S rRNA gene sequence data stemming from high-throughput amplicon pyrosequencing of rumen-derived DNA samples. The 18S rRNA gene-based ciliate community structure was compared to that obtained from microscopic counts using the same samples. Both methods allowed identification of dominant members of the ciliate communities and classification of the rumen ciliate community into one of the types first described by Eadie in 1962. Notably, each method is associated with advantages and disadvantages. Microscopy is a highly accurate method for evaluation of total numbers or relative abundances of different ciliate genera in a sample, while 18S rRNA gene pyrosequencing represents a valuable alternative for comparison of ciliate community structure in a large number of samples from different animals or treatment groups.

Reisolation and redescription of Balantidium duodeni Stein, 1867 (Litostomatea, Trichostomatia)

In this work, we present reisolation and redescription of Balantidium duodeni Stein, 1867 from the European common brown frog Rana temporaria Linnaeus, 1758 using light and electron microscopy. This species has a unique morphological feature--its cells are flattened along the dorsoventral axis. Because of its unique morphology and localization (duodenum) in the gastrointestinal tract of the host, it has been proposed to recognize B. duodeni as a member of separate genus, Balantidiopsis Penard, 1922. Molecular phylogenetic analysis demonstrates it to be close to the type species Balantidium entozoon (Ehrenberg, 1838). We argue that its placement into separate genus is not substantiated. We also propose to reinstate the genus Balantioides Alexeieff, 1931 with the type species Paramecium coli (Malmstein, 1857). The recently proposed generic name for this taxon, Neobalantidium Pomajbíková et al., 2013, is a junior synonym of the previously recognized name.