Rumen Ciliated Protozoa of the Free-Living European Bison (Bison bonasus, Linnaeus)

This study aims to perform population analysis of the rumen ciliated protozoa of the free-living European bison (wisent, Bison bonasus, Linnaeus). The samples of the rumen fluid from the 18 bison subjected to the controlled culls within the free-ranging population in the Bialowieza primeval forest in Poland were collected and examined. The examined ciliates population consisted of the species of the families Isotrichidae and Ophryoscolecidae. There were 12 genera (Isotricha, Dasytricha, Diplodinium, Elytroplastron, Entodinium, Eodinium, Epidinium, Eremoplastron, Eudiplodinium, Metadinium, Ophryoscolex, and Ostracodinium) and 32 morphospecies of the ciliates. We observed the prevalence of a type B protozoan population (56% animals) with the typical Epidinium and Eudiplodinium genera members. Other examined animals possessed the mixed A–B population with Ophryoscolex genus, distinct for type A ciliate population. The average total ciliates count was 2.77 ± 1.03 × 105/ml (mean ± SD). The most abundant genera were Entodinium, 83%, and Dasytricha, 14%. The abundance of other genera was <1% of the total count. Within the 16 Entodinium species determined, the most abundant species was Entodinium nanellum (16.3% of total ciliates count). The average Shannon–Wiener diversity index was 2.1 ± 0.39, evenness was 0.7 ± 0.11, and species richness was 24 ± 3.0 (mean ± SD). Our study is the first report on the population composition and diversity of rumen ciliates of European bison. The composition and counts of ciliate genera and species were similar to the composition and counts of the rumen ciliated protozoa of American bison and many other kinds of free-living and domestic ruminants. Our European bison ciliate population analysis has shown medium ciliate density and high diversity typical for large free-living ruminants with mixed feeding behavior.

Bacteria-Derived Hemolysis-Related Genes Widely Exist in Scuticociliates

Scuticociliatosis is an invasive external or systemic infection caused by ciliated protozoa, mainly those within the subclass Scuticociliatia (scuticociliates). Many scuticociliates are fish pathogens, including Miamiensis avidus, Philasterides dicentrarchi, Pseudocohnilembus persalinus, and Uronema marinum. Our previous study showed that hemolysis-related genes derived from bacteria through horizontal gene transfer (HGT) may contribute to virulence in P. persalinus. Hemorrhagic lesions are a common feature of scuticociliatosis, but it is not known whether other scuticociliates also have bacteria-derived hemolysis-related genes. In this study, we constructed a high-quality macronuclear genome of another typical pathogenic scuticociliate, U. marinum. A total of 105 HGT genes were identified in this species, of which 35 were homologs of hemolysis-related genes (including hemolysin-like genes) that had previously been identified in P. persalinus. Sequencing of an additional five species from four scuticociliate families showed that bacteria-derived hemolysis-related genes (especially hemolysin-like genes) are widely distributed in scuticociliates. Based on these findings, we suggest that hemolysin-like genes may have originated before the divergence of scuticociliates.

Uptake of plastic microbeads by ciliate Paramecium aurelia

Microplastics (MPs) are small fraction of plastics that are less than 5 mm in length. They are bountiful and widespread pollutants in the aquatic environment. A wide range of organisms which play an important role in the food web, ingest microplastic particles and transfer them to the higher trophic levels. In this work, ingestion of fluorescent polystyrene beads 2 µm of diameter by ciliated protozoa Paramecium aurelia in different concentrations and times of exposure was studied. We studied also the ingestion and clearance rate as well as formation of food vacuoles. The highest uptake of beads by ciliates reached 1047.2 ± 414.46 particles after 10 min of incubation. Food vacuoles formation reflected the ingestion rate of P. aurelia, which increased at higher beads concentration up to the10th minute of incubation and decreased afterwards. On the contrary, the clearance rate persisted to be higher at low concentration. These findings showed that maximum capacity of microplastics ingestion by paramecia depended on beads concentration and on time of exposure.

Oxygen Gradients and Structure of the Ciliate Assemblages in Floodplain Lake

This paper presents the results of studies on the structure of the ciliate population in a freshwater lake. The classification of the ciliated communities based on the analysis of the distribution of ciliate population density in the lake along the oxygen gradients, taking into account their oxygen preferences, was proposed. It was shown that the distribution of ciliated protozoa in the space of a reservoir is determined not by such spatial units as the water column, bottom, and periphytal, but by the oxygen gradients. Four types of habitats with different oxygen regimes were distinguished: With stably high oxygen concentration, stably low oxygen concentration, stably oxygen-free conditions, and conditions with a high amplitude of diurnal oxygen variations. The location of these habitats in the space of the lake and their seasonal changes were determined. On the basis of the quantitative development of ciliate populations, zones of optima and tolerance ranges of some ciliate species in the oxygen gradient were established. The oxygen preferences were established for the species from four distinguished assemblages: Microoxyphilic, oxyphilic, euryoxyphilic, and anoxyphilic (anaerobic). The presence or the absence of a certain type of assemblage in the reservoirs depends solely on the parameters of the oxygen gradients. The diversity of the ciliated protozoa in water bodies also depends on the stability and diversity of the oxygen gradients.

The Encystment-Related MicroRNAs and Its Regulation Molecular Mechanism in Pseudourostyla cristata Revealed by High Throughput Small RNA Sequencing

MicroRNAs (miRNAs) regulate the expression of target genes in diverse cellular processes and play important roles in different physiological processes. However, little is known about the microRNAome (miRNAome) during encystment of ciliated protozoa. In the current study, we first investigated the differentially expressed miRNAs and relative signaling pathways participating in the transformation of vegetative cells into dormant cysts of Pseudourostyla cristata (P. cristata). A total of 1608 known miRNAs were found in the two libraries. There were 165 miRNAs with 1217 target miRNAs. The total number of differential miRNAs screened between vegetative cells and dormant cysts databases were 449 with p < 0.05 and |log2 fold changes| > 1. Among them, the upregulated and downregulated miRNAs were 243 and 206, respectively. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that some of the differentially expressed miRNAs were mainly associated with oxidative phosphorylation, two-component system, and biosynthesis of amino acids. Combining with our bioinformatics analyzes, some differentially expressed miRNAs including miR-143, miR-23b-3p, miR-28, and miR-744-5p participates in the encystment of P. cristata. Based on these findings, we propose a hypothetical signaling network of miRNAs regulating or promoting P. cristata encystment. This study shed new lights on the regulatory mechanisms of miRNAs in encystment of ciliated protozoa.

Spatial patterns of functional diversity and composition in marine benthic ciliates along the coast of China

Large-scale patterns of community composition and diversity along environmental gradients have been well studied for macroorganisms. However, the biogeography of microorganisms, especially ciliated protozoa, remains understudied. Here, we analyzed a comprehensive database of marine benthic ciliates found along the coast of China from 1991 to 2018 to examine the geographical patterns in species and trait composition and functional diversity. According to redundancy analysis conducted at large spatial scales, environmental variables, i.e. habitat type and salinity, explained more variance in species composition than latitude. In contrast, trait composition was better explained by spatial and climatic variables. At small spatial scales, both species and trait composition were probably influenced by mass effects due to the high dispersal ability of ciliates at such small scales, resulting in spatially homogenized communities. Several traits, including body size, feeding type and mobility, exhibited significant positive or negative latitudinal gradients. Functional diversity showed a significant positive correlation with latitude between 20 and 40° N, which may be caused by certain groups of ciliates possessing particular traits related to temperature. Our study is the first comprehensive evaluation of how trait composition and functional diversity of marine ciliated protozoa vary at large scales and can thus make a major contribution to the study of microbial biogeography.

Diversification of small RNA amplification mechanisms for targeting transposon-related sequences in ciliates

The silencing of repetitive transposable elements (TEs) is ensured by signal amplification of the initial small RNA trigger, which occurs at distinct steps of TE silencing in different eukaryotes. How such a variety of secondary small RNA biogenesis mechanisms has evolved has not been thoroughly elucidated. Ciliated protozoa perform small RNA-directed programmed DNA elimination of thousands of TE-related internal eliminated sequences (IESs) in the newly developed somatic nucleus. In the ciliate Paramecium, secondary small RNAs are produced after the excision of IESs. In this study, we show that in another ciliate, Tetrahymena, secondary small RNAs accumulate at least a few hours before their derived IESs are excised. We also demonstrate that DNA excision is dispensable for their biogenesis in this ciliate. Therefore, unlike in Paramecium, small RNA amplification occurs before IES excision in Tetrahymena. This study reveals the remarkable diversity of secondary small RNA biogenesis mechanisms, even among ciliates with similar DNA elimination processes, and thus raises the possibility that the evolution of TE-targeting small RNA amplification can be traced by investigating the DNA elimination mechanisms of ciliates.