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Eukaryotic cells depend on dynamic changes in shape to fulfill a wide range of cellular functions, maintain essential biological processes, and regulate cellular behavior. The single-celled, predatory ciliate Lacrymaria exhibits extraordinary dynamic shape-shifting using a flexible "neck" that can stretch 7–8 times the length of its body to capture prey. The molecular mechanism behind this morphological change remains a mystery. We have observed that when in an active state, Lacrymaria repeatedly extends and contracts its neck to enable 360-degree space search and prey capture. This remarkable morphological change involves a unique actin-myosin system rather than the Ca2+-dependent system found in other contractile ciliates. Two cytoskeletons are identified in the cortex of the Lacrymaria cell, namely the myoneme cytoskeleton and the microtubule cytoskeleton. The myoneme cytoskeleton is composed of centrin-myosin proteins, exhibiting distinct patterns between the neck and body, with their boundary seemingly associated with the position of the macronucleus. A novel giant protein forming a ladder-like structure was discovered as a component of the microtubule cytoskeleton. Thick centrin-myosin fibers are situated very close to the right side of the ladders in the neck but are far away from such structures in the body. This arrangement enables the decoupling of the neck and body. Plasmodium -like unconventional actin has been discovered in Lacrymaria , and this may form highly dynamic short filaments that could attach to the giant protein and myosin, facilitating coordination between the two cytoskeletons in the neck. In summary, this fascinating organism employs unconventional cytoskeletal components to accomplish its extraordinary dynamic shape-shifting. [Display omitted] • Lacrymaria uses a unique actin-myosin system for neck morphology changes • Two cytoskeletal structures with unconventional components work together • The centrin-myosin-based myoneme shows distinct patterns in neck and body • A giant protein forms a ladder structure in the microtubule cytoskeleton Qin et al. discover the mechanism behind the remarkable shape-shifting of the unicellular predator, Lacrymaria. They identify two key cytoskeletal structures: a centrin-myosin-based myoneme and a giant protein-containing microtubule cytoskeleton. These structures work together to decouple the neck and body, enabling its dynamic neck morphology. [ABSTRACT FROM AUTHOR]

The perception of the importance of ciliate in freshwater has changed dramatically since the "microbial loop" conceptualisation, reflecting methodological attempts. The data from two decades (1994–2018) on the surface (0–3 m) ciliate assemblage in the Slapy reservoir (Vltava River, Czech Republic) during two different nutrient-load defined periods were analysed. We grouped the identified, quantified, and biomass-evaluated ciliates in the quantitative protargol-impregnated preparations according to their feeding behaviour. The sampling median and interquartile range data of the ciliates were plotted; the modelled water age, nutrients, bacteria, heterotrophic nanoflagellates, and Rhodomonas spp. were applied as the main explanatory background variables. We validated the differences between the periods, engaging multivariate analyses. The picoplankton-filtering species dominated the assemblages in an annual mean (halteriids and minute strobilidiids followed by peritrichs). Algae hunting urotrichs, Balanion planctonicum, and nanoplankton filtering tintinnids were significant before the spring phytoplankton peak when a maximum of ciliate biomass reflected mixotrophic nanoplankton filtering pelagostrombidiids. Only there did ciliate biomass tightly follow their quantified prey. Heterotrophic and mixotrophic Askenasia and Lagynophrya were typical raptorial/flagellate-hunting cilates; only Mesodinium spp. reached the maximum during autumn. The observed oligotrophication of the reservoir increased the ciliate assemblage biomass in the surface layer during stratification in concordance with the Plankton Ecology Group (PEG) model. [ABSTRACT FROM AUTHOR]

Ciliated microeukaryotes (ciliates) are distinguished by their cilia, which are rich in tubulin. We developed a method for tubulin staining in ciliate cells that involves using live-cell tubulin-staining dyes instead of antibodies thereby streamlining the staining process, which is effective across diverse ciliate lineages. Moreover, our method allows integration with immunofluorescence staining using antibodies when needed. The potential applications of this technique extend to cell biology and ciliate morphological and ecological studies. [ABSTRACT FROM AUTHOR]

Vorticella convallaria are microscopic sessile suspension feeders that live attached to substrates in aquatic environments. They feed using a self‐generated current and help maintain the health of aquatic ecosystems and wastewater treatment facilities by consuming bacteria and detritus. Their environmental impact is mediated by their feeding rate. In ambient flow, feeding rates are highly dependent on an individual's orientation relative to the substrate and the flow. Here, we investigate how this orientation is impacted by flow speed. Furthermore, we examined whether individuals actively avoid orientations unfavorable for feeding. We exposed individuals to unidirectional laminar flow at shear rates of 0, 0.5, 1.0, and 1.5 s−1, and recorded their 3D orientation using a custom biplanar microscope. We determined that V. convallaria orientation became progressively tilted downstream as the shear rate increased, but individuals were still able to actively reorient. Additionally, at higher shear rates, individuals spent a larger fraction of their time in orientations with reduced feeding rates. Our shear rates correspond to freestream flows on the scale of mm s−1 to cm s−1 in natural environments. [ABSTRACT FROM AUTHOR]

Ciliates assemble numerous microtubular structures into complex cortical patterns. During ciliate division, the pattern is duplicated by intracellular segmentation that produces a tandem of daughter cells. In Tetrahymena thermophila, the induction and positioning of the division boundary involves two mutually antagonistic factors: posterior CdaA (cyclin E) and anterior CdaI (Hippo kinase). Here, we characterized the related cdaH-1 allele, which confers a pleiotropic patterning phenotype including an absence of the division boundary and an anterior-posterior mispositioning of the new oral apparatus. CdaH is a Fused or Stk36 kinase ortholog that localizes to multiple sites that correlate with the effects of its loss, including the division boundary and the new oral apparatus. CdaH acts downstream of CdaA to induce the division boundary and drives asymmetric cytokinesis at the tip of the posterior daughter. CdaH both maintains the anterior-posterior position of the new oral apparatus and interacts with CdaI to pattern ciliary rows within the oral apparatus. Thus, CdaH acts at multiple scales, from induction and positioning of structures on the cell-wide polarity axis to local organelle-level patterning. [ABSTRACT FROM AUTHOR]

Endosymbiosis is a widespread and important phenomenon requiring diverse model systems. Ciliates are a widespread group of protists that often form symbioses with diverse microorganisms. Endosymbioses between the ciliate Euplotes and heritable bacterial symbionts are common in nature, and four essential symbionts were described: Polynucleobacter necessarius, “Candidatus Protistobacter heckmanni,” “Ca. Devosia symbiotica,” and “Ca. Devosia euplotis.” Among them, only the genus Polynucleobacter comprises very close free-living and symbiotic representatives, which makes it an excellent model for investigating symbiont replacements and recent symbioses. In this article, we characterized a novel endosymbiont inhabiting the cytoplasm of Euplotes octocarinatus and found that it is a close relative of the free-living bacterium Fluviibacter phosphoraccumulans (Betaproteobacteria and Rhodocyclales). We present the complete genome sequence and annotation of the symbiotic Fluviibacter. Comparative analyses indicate that the genome of symbiotic Fluviibacter is small in size and rich in pseudogenes when compared with free-living strains, which seems to fit the prediction for recently established endosymbionts undergoing genome erosion. Further comparative analysis revealed reduced metabolic capacities in symbiotic Fluviibacter, which implies that the symbiont relies on the host Euplotes for carbon sources, organic nitrogen and sulfur, and some cofactors. We also estimated substitution rates between symbiotic and free-living Fluviibacter pairs for 233 genes; the results showed that symbiotic Fluviibacter displays higher dN/dS mean value than free-living relatives, which suggested that genetic drift is the main driving force behind molecular evolution in endosymbionts. IMPORTANCE In the long history of symbiosis research, most studies focused mainly on organelles or bacteria within multicellular hosts. The single-celled protists receive little attention despite harboring an immense diversity of symbiotic associations with bacteria and archaea. One subgroup of the ciliate Euplotes species is strictly dependent on essential symbionts for survival and has emerged as a valuable model for understanding symbiont replacements and recent symbioses. However, almost all of our knowledge about the evolution and functions of Euplotes symbioses comes from the Euplotes– Polynucleobacter system. In this article, we report a novel essential symbiont, which also has very close free-living relatives. Genome analysis indicated that it is a recently established endosymbiont undergoing genome erosion and relies on the Euplotes host for many essential molecules. Our results provide support for the notion that essential symbionts of the ciliate Euplotes evolve from free-living progenitors in the natural water environment. [ABSTRACT FROM AUTHOR]

Unicellular ciliates like Tetrahymena are best known as free-living bacteriovores, but many species are facultative or obligate parasites. These "histophages" feed on the tissues of hosts ranging from planarian flatworms to commercially important fish and the larvae of imperiled freshwater mussels. Here, we developed a novel bioinformatics pipeline incorporating the nonstandard ciliate genetic code and used it to search for Ciliophora sequences in 34 publicly available Platyhelminthes EST libraries. From 2,615,036 screened ESTs, we identified nearly 6,000 high-confidence ciliate transcripts, supporting parasitism of seven additional flatworm species. We also cultured and identified Tetrahymena from nine terrestrial and freshwater planarians, including invasive earthworm predators from the genus Bipalium and the widely studied regeneration models Dugesia japonica and Schmidtea mediterranea. A co-phylogenetic reconstruction provides strong evidence for the coevolution of histophagous Ciliophora with their Platyhelminthes hosts. We further report the antiprotozoal aminoglycoside paromomycin expels Tetrahymena from S. mediterranea , providing new opportunities to investigate the effects of this relationship on planarian biology. Together, our findings raise the possibility that invasive flatworms constitute a novel dispersal mechanism for Tetrahymena parasites and position the Platyhelminthes as an ideal model phylum for studying the ecology and evolution of histophagous ciliates. [ABSTRACT FROM AUTHOR]

Background: Hosts, parasites, and microbiota interact with each other, forming a complex ecosystem. Alterations to the microbial structure have been observed in various enteric parasitic infections (e.g. parasitic protists and helminths). Interestingly, some parasites are associated with healthy gut microbiota linked to the intestinal eubiosis state. So the changes in bacteria and metabolites induced by parasite infection may offer benefits to the host, including protection from other parasitesand promotion of intestinal health. The only ciliate known to inhabit the hindgut of grass carp, Balantidium ctenopharyngodoni, does not cause obvious damage to the intestinal mucosa. To date, its impact on intestinal microbiota composition remains unknown. In this study, we investigated the microbial composition in the hindgut of grass carp infected with B. ctenopharyngodoni, as well as the changes of metabolites in intestinal contents resulting from infection. Results: Colonization by B. ctenopharyngodoni was associated with an increase in bacterial diversity, a higher relative abundance of Clostridium, and a lower abundance of Enterobacteriaceae. The family Aeromonadaceae and the genus Citrobacter had significantly lower relative abundance in infected fish. Additionally, grass carp infected with B. ctenopharyngodoni exhibited a significant increase in creatine content in the hindgut. This suggested that the presence of B. ctenopharyngodoni may improve intestinal health through changes in microbiota and metabolites. Conclusions: We found that grass carp infected with B. ctenopharyngodoni exhibit a healthy microbiota with an increased bacterial diversity. The results suggested that B. ctenopharyngodoni reshaped the composition of hindgut microbiota similarly to other protists with low pathogenicity. The shifts in the microbiota and metabolites during the colonization and proliferation of B. ctenopharyngodoni indicated that it may provide positive effects in the hindgut of grass carp. [ABSTRACT FROM AUTHOR]

The subclass Cyrtophoria is a group of morphologically specialized ciliates with diverse characteristics, which can be found in a variety of aquatic and terrestrial habitats. In the present study, two cyrtophorian ciliates, Aegyria oliva Claparède & Lachmann, 1859 and A. peculiaris sp. nov., isolated from coastal waters of China, were investigated based on microscopic observations of live and protargol-stained specimens, and SSU rRNA gene sequence analyses. For A. oliva, the type species of the genus, detailed morphometric data, and improved diagnosis are provided. The new species, Aegyria peculiaris sp. nov. is characterized by a body size of 70–115 × 30–65 μm in vivo, an inverted oval body shape with a protrusion at the anterior left and a posterior bulge on the dorsal side, 45–58 somatic kineties, 31–46 nematodesmal rods, 4–6 transpodial segments, and about six contractile vacuoles. Phylogenetic analyses unveiled a close relationship between the newly identified species and A. foissneri, thereby confirming the monophyly of the genus Aegyria. [ABSTRACT FROM AUTHOR]

The mortality rate of red-tide dinoflagellates owing to predation is a major parameter that affects their population dynamics. The dinoflagellates Ansanella granifera and Ansanella sp. occasionally cause red tides. To understand the interactions between common heterotrophic protists and A. granifera, we explored the feeding occurrence of nine heterotrophic protists on A. granifera and the growth and ingestion rates of the heterotrophic dinoflagellate Gyrodinium dominans on A. granifera as a function of prey concentration and those of Oxyrrhis marina at a single high prey concentration. The heterotrophic dinoflagellates Aduncodinium glandula, G. dominans, Gyrodinium moestrupii, Luciella masanensis, Oblea rotunda, O. marina, Polykrikos kofoidii, and Pfiesteria piscicida and the naked ciliate Strombidium sp. were able to feed on A. granifera. With increasing mean prey concentrations, the growth and ingestion rates of G. dominans feeding on A. granifera rapidly increased and became saturated or slowly increased. The maximum growth and ingestion rates of G. dominans on A. granifera were 0.305 d-1 and 0.42 ng C predator-1 d-1 (3.8 cells predator-1 d-1), respectively. Furthermore, the growth and ingestion rates of O. marina on A. granifera at 1,700 ng C mL-1 (15,454 cells mL-1) were 0.037 d-1 and 0.19 ng C predator-1 d-1 (1.7 cells predator-1 d-1), respectively. The growth and ingestion rates of G. dominans and O. marina feeding on A. granifera were almost the lowest among those on the dinoflagellate prey species. Therefore, G. dominans and O. marina may prefer A. granifera less than other dinoflagellate prey species. The low mortality rate of A. granifera may positively affect its bloom formation. [ABSTRACT FROM AUTHOR]

Our knowledge of ciliate endosymbiont diversity greatly expanded over the past decades due to the development of characterization methods for uncultivable bacteria. Chlamydia‐like bacteria have been described as symbionts of free‐living amoebae and other phylogenetically diverse eukaryotic hosts. In the present work, a systematic survey of the bacterial diversity associated with the ciliate Euplotes octocarinatus strain Zam5b‐1 was performed, using metagenomic screening as well as classical full‐cycle rRNA approach, and a novel chlamydial symbiont was characterized. The metagenomic screening revealed 16S rRNA gene sequences from Polynucleobacter necessarius, three previously reported accessory symbionts, and a novel chlamydia‐like bacterium. Following the full‐cycle rRNA approach, we obtained the full‐length 16S rRNA gene sequence of this chlamydia‐like bacterium and developed probes for diagnostic fluorescence in situ hybridizations. The phylogenetic analysis of the 16S rRNA gene sequences unambiguously places the new bacterium in the family Rhabdochlamydiaceae. This is the first report of chlamydia‐like bacterium being found in Euplotes. Based on the obtained data, the bacterium is proposed as a new candidate genus and species: "Candidatus Euplotechlamydia quinta." [ABSTRACT FROM AUTHOR]

G protein-coupled receptors (GPCRs) are the largest family of transmembrane receptors and play important roles in many physiological processes. As a representative group of protozoa, ciliates represent the highest stage of eukaryotic cell differentiation and evolution in terms of their reproductive mode, two-state karyotype, and extremely diverse cytogenesis patterns. GPCRs have been poorly reported in ciliates. In this study, we identified 492 GPCRs in 24 ciliates. Using the existing classification system for animals, GPCRs in ciliates can be assigned to four families, including families A, B, E, and F. Most (377 members) belong to family A. The number of GPCRs is extremely different in different ciliates; the Heterotrichea ciliates usually have more GPCRs than other ciliates. Parasitic or symbiotic ciliates usually have only a few GPCRs. Gene/genome duplication events seem to play important roles in the expansion of the GPCR superfamily in ciliates. GPCRs in ciliates displayed seven typical domain organizations. GPCRs in an ortholog group are common and conserved in all ciliates. The gene expression analysis of the members in this conserved ortholog group in the model ciliate, Tetrahymena thermophila, suggested that these GPCRs play important roles in the life cycle of ciliates. In summary, this study provides the first comprehensive genome-wide identification of GPCRs in ciliates, improving our understanding of the evolution and function of GPCR in ciliates. [ABSTRACT FROM AUTHOR]

Most eukaryotes employ a combination of transcriptional and post-transcriptional silencing mechanisms to suppress transposons, yet ciliates employ a more extreme approach. They separate germline and somatic functions into distinct nuclei, enabling the elimination of transposons from the active somatic genome through diverse small RNA-mediated genome rearrangement pathways during sexual processes. [ABSTRACT FROM AUTHOR]

Resting cyst formation is a crucial process of cryptobiosis in protists. In colpodid ciliates, cyst formation is accompanied by largescale morphological changes such as changes of cell shape, resorption of cilia, and formation of a cyst wall; additionally, the cell cycle is arrested. These changes provide acquired tolerance against environmental stresses. During cyst formation, mitochondrial membrane potential is reduced and the level of the ATP synthase beta chain is suppressed, strongly indicating that metabolism has ceased. Here, however, we show that ATP levels are elevated during the initial phases of encystment implying that metabolism may not be completely suppressed. This finding suggests another aspect of resting cyst formation that is not applicable to cryptobiosis. [ABSTRACT FROM AUTHOR]

Periphytic ciliates play a vital role in the material cycle and energy flow of microbial food web, however, their taxonomy and biodiversity are inadequately studied given their high species richness. Two new and one little known species, viz. Derouxella lembodes gen. et sp. nov., Cyrtophoron multivacuolatum sp. nov., and Cyrtophoron apsheronica Aliev, 1991, collected from coastal waters of China, were investigated using modern methods. Derouxella gen. nov. can be recognized by having dorsoventrally flattened body, a podite, one fragmented preoral kinety, two parallel circumoral kineties, and somatic kineties progressively shortened from right to left. Morphological classification and phylogenetic analyses based on nuclear small subunit ribosomal RNA (nSSU rRNA) and mitochondrial small subunit ribosomal RNA (mtSSU rRNA) gene sequence data inferred that Derouxella gen. nov. occupies an intermediate position between Hartmannulidae and Dysteriidae. Cyrtophoron multivacuolatum sp. nov. is characterized by large body size, the numbers of somatic kineties and nematodesmal rods, and having numerous contractile vacuoles. The genus Cyrtophoron and the poorly known species C. apsheronica were redefined. Even with the addition of newly obtained nSSU rRNA and mtSSU rRNA gene sequences of Cyrtophoron, the family Chlamydodontidae was still recovered as a monophyletic group, the monophyly of Cyrtophoron was supported too. [ABSTRACT FROM AUTHOR]

Parasite conservation is important for the maintenance of ecosystem diversity and function. Conserving parasites relies first on understanding parasite biodiversity and second on estimating the extinction risk to that biodiversity. Although steps have been taken independently in both these areas, previous studies have overwhelmingly focused on helminths in vertebrate hosts over broad scales, providing low resolution and excluding a large proportion of possible host and parasite diversity. We estimated both total obligate parasite richness and parasite extinction risk in freshwater mussels (Unionidae and Margaritiferidae) from Europe and the United States to provide a case study for considering parasite conservation in a severely understudied system. We used currently reported host–parasite relationships to extrapolate parasite diversity to all possible mussel hosts and then used the threat levels of those hosts to estimate the extinction risk for both described and undescribed parasites. An estimated 67% of parasite richness in freshwater mussels is undescribed and over 80% of the most host‐specific groups (digenean trematodes and ciliates) are undescribed. We estimated that 21% of this total parasite fauna is at immediate risk of extinction, corresponding to 60 unique species, many of which will likely go extinct before being described. Given the important roles parasites play in community structure and function and the strong ecosystem engineering capacities of freshwater mussels, such extinctions are likely to severely affect freshwater ecosystems. Our detailed study of mussel parasites provides compelling evidence for the hidden conservation threat to parasites through extinction cascades and shows parasites are deserving of immediate attention. Article Impact Statement: Two‐thirds of freshwater mussel parasites are undescribed and over one‐fifth are at immediate risk of extinction. [ABSTRACT FROM AUTHOR]

The purpose of this study is to determine which taxonomic methods can elucidate clear and quantifiable differences between two cryptic ciliate species, and to test the utility of genome architecture as a new diagnostic character in the discrimination of otherwise indistinguishable taxa. Two cryptic tintinnid ciliates, Schmidingerella arcuata and Schmidingerella meunieri, are compared via traditional taxonomic characters including lorica morphometrics, ribosomal RNA (rRNA) gene barcodes and ecophysiological traits. In addition, single‐cell 'omics analyses (single‐cell transcriptomics and genomics) are used to elucidate and compare patterns of micronuclear genome architecture between the congeners. The results include a highly similar lorica that is larger in S. meunieri, a 0%–0.5% difference in rRNA gene barcodes, two different and nine indistinguishable growth responses among 11 prey treatments, and distinct patterns of micronuclear genomic architecture for genes detected in both ciliates. Together, these results indicate that while minor differences exist between S. arcuata and S. meunieri in common indices of taxonomic identification (i.e., lorica morphology, DNA barcode sequences and ecophysiology), differences exist in their genomic architecture, which suggests potential genetic incompatibility. Different patterns of micronuclear architecture in genes shared by both isolates also enable the design of species‐specific primers, which are used in this study as unique "architectural barcodes" to demonstrate the co‐occurrence of both ciliates in samples collected from a NW Atlantic estuary. These results support the utility of genomic architecture as a tool in species delineation, especially in ciliates that are cryptic or otherwise difficult to differentiate using traditional methods of identification. [ABSTRACT FROM AUTHOR]

Heavily melanized gills in crustaceans, often referred to as black gill, have been reported in both wild and cultured marine species. Tissue melanization is generally the result of a response of the crustacean innate immune system to the presence of an irritant or pathogen. While black gill can be caused by a variety of abiotic stressors and nutritional deficiencies, biotic agents are the cause of most reported black gill cases in crustaceans. In high density culture systems, fungi are identified as the most common causes of black gill outbreaks. In the wild, epidemic-scale outbreaks of black gill appear largely to be caused by ciliate rather than fungal infections. Black gill epidemics caused by ciliates have recently been reported in two commercially important fishery species including penaeid shrimp in the South Atlantic Bight USA (Western North Atlantic) and the Gulf of Mexico, and in pandalid shrimp in the Gulf of Maine, USA. Here we review the reports of the occurrence, causative agents, biology, ecology, and impacts of black gill on wild crustacean species of black gill with special focus on the pandalid shrimp species Pandalus borealis parasitized by the apostome ciliate Synophrya sp. and penaeid shrimp in the Western North Atlantic and Gulf of Mexico parasitized by a newly described apostome ciliate species Hyalophysa lynni. A review of the literature reveals large knowledge gaps with respect to black gill in both commercially exploited and other keystone crustacean species. Recommendations for future research include improved surveillance and identification of causative agents of black gill, improved understanding of their interactions with crustacean hosts including distribution, transmission, morbidity, and mortality, epidemiology, molecular biology, and relationship with climate. [ABSTRACT FROM AUTHOR]

Holotrichous ciliates, like Paramecium, swim through their aqueous environment by beating their many cilia. They can alter swimming speed and direction, which seems to have mesmerized early microscopists of the 1600s. We know from extensive and elegant physiological studies and generation of mutants that these cells can be considered little swimming neurons because their ciliary beating is under bioelectric control of ion channels in the cilia. This chapter will focus on the ionic control of swimming behavior by ciliary ion channels, primarily in the holotrichous ciliate Paramecium. Voltage‐gated and calcium‐activated channels for calcium, magnesium, sodium, and potassium are regulated in a closely orchestrated manner that allows cilia to bend and propel the cell forward or backward. Sensory input that generates receptor potentials feeds into the control of this channel activity and allows the cell to turn or speed up. This in turn helps the cell to avoid predators or toxic conditions. While the focus is on P. tetraurelia and P. caudatum, the principles of ciliary ion channel activity and control are easily extendable to other ciliates and protists. The high conservation of channel and ion pump structures also extends the lessons from Paramecium to higher organisms. [ABSTRACT FROM AUTHOR]

The term epigenetics is used for any layer of genetic information aside from the DNA base‐sequence information. Mammalian epigenetic research increased our understanding of chromatin dynamics in terms of cytosine methylation and histone modification during differentiation, aging, and disease. Instead, ciliate epigenetics focused more on small RNA‐mediated effects. On the one hand, these do concern the transport of RNA from parental to daughter nuclei, representing a regulated transfer of epigenetic information across generations. On the other hand, studies of Paramecium, Tetrahymena, Oxytricha, and Stylonychia revealed an almost unique function of transgenerational RNA. Rather than solely controlling chromatin dynamics, they control sexual progeny's DNA content quantitatively and qualitatively. Thus epigenetics seems to control genetics, at least genetics of the vegetative macronucleus. This combination offers ciliates, in particular, an epigenetically controlled genetic variability. This review summarizes the epigenetic mechanisms that contribute to macronuclear heterogeneity and relates these to nuclear dimorphism. This system's adaptive and evolutionary possibilities raise the critical question of whether such a system is limited to unicellular organisms or binuclear cells. We discuss here the relevance of ciliate genetics and epigenetics to multicellular organisms. [ABSTRACT FROM AUTHOR]

Ciliates are defined by the presence of dimorphic nuclei as they have both a somatic macronucleus and germline micronucleus within each individual cell. The size and structure of both germline micronuclei and somatic macronuclei vary tremendously among ciliates. Except just after conjugation (i.e. the nuclear exchange in their life cycle), the germline micronucleus is transcriptionally inactive and contains canonical chromosomes that will be inherited between generations. In contrast, the transcriptionally active macronucleus contains chromosomes that vary in size in different classes of ciliates, with some lineages having extensively fragmented gene‐sized somatic chromosomes while others contain longer multigene chromosomes. Here, we describe the variation in somatic macronuclear architecture in lineages sampled across the ciliate tree of life, specifically focusing on lineages with extensively fragmented chromosomes (e.g. the classes Phyllopharyngea and Spirotrichea). Further, we synthesize information from the literature on the development of ciliate macronuclei, focusing on changes in nuclear architecture throughout life cycles. These data highlight the tremendous diversity among ciliate nuclear cycles, extend our understanding of patterns of genome evolution, and provide insight into different germline and somatic nuclear features (e.g. nuclear structure and development) among eukaryotes. [ABSTRACT FROM AUTHOR]

Mobile genetic elements (MGEs) are transient genetic material that can move either within a single organism's genome or between individuals or species. While historically considered "junk" DNA (i.e., deleterious or at best neutral), more recent studies reveal the potential adaptive advantages MGEs provide in lineages across the tree of life. Ciliates, a group of single‐celled microbial eukaryotes characterized by nuclear dimorphism, exemplify how epigenetic influences from MGEs shape genome architecture and patterns of molecular evolution. Ciliate nuclear dimorphism may have evolved as a response to transposon invasion and ciliates have since co‐opted transposons to carry out programmed DNA deletion. Another example of the effect of MGEs is in providing mechanisms for lateral gene transfer (LGT) from bacteria, which introduces genetic diversity and, in several cases, may drive ecological specialization in ciliates. As a third example, the integration of viral DNA, likely through transduction, provides new genetic materials and can change the way host cells defend themselves against other viral pathogens. We argue that the acquisition of MGEs through non‐Mendelian patterns of inheritance, coupled with their effects on ciliate genome architecture and persistence throughout evolutionary history, exemplify how the transmission of mobile elements should be considered a mechanism of transgenerational epigenetic inheritance. [ABSTRACT FROM AUTHOR]

The generation of efficient fluid flow is crucial for organismal development and homeostasis, sexual reproduction, and motility. Multi‐ciliated cells possess fields of motile cilia that beat in synchrony to propel fluid. Ciliary arrays are remarkably conserved in their organization and function. Ciliates have polarized multi‐ciliary arrays (MCAs) to promote fluid flow for cell motility. The ciliate cortex is decorated with hundreds of basal bodies (BB) forming linear rows along the cellʼs anterior–posterior axis. BBs scaffold and position cilia to form the organized ciliary array. Nascent BBs assemble at the base of BBs. As nascent BBs mature, they integrate into the cortical BB and cytoskeletal network and nucleate their own cilium. The organization of MCAs is balanced between cortical stability and cortical dynamism. The cortical cytoskeletal network both establishes and maintains a stable organization of the MCA in the face of mechanical forces exerted by ciliary beating. At the same time, MCA organization is plastic, such that it remodels for optimal ciliary mobility during development and in response to environmental conditions. Such plasticity promotes effective feeding and ecological behavior required for these organisms. Together, these properties allow an organism to effectively sense, adapt to, and move through its environment. [ABSTRACT FROM AUTHOR]

The propagule sizes of these green seaweeds were ca. 3-10 m. Ciliates feeding on seaweed propagules were observed even when other known foods, such as diatoms and phytoflagellates, were available. I Monostroma i propagules measure 5-10 m, swim using flagella, and settle on benthic substrates; these characteristics resemble those of the propagules of many other green seaweed species. Keywords: ciliate; coastal ecosystem; food web; green seaweed; life history; microscopic grazer; population dynamics; propagule survival EN ciliate coastal ecosystem food web green seaweed life history microscopic grazer population dynamics propagule survival 1 5 5 08/03/22 20220801 NES 220801 Seaweeds, such as green (Ulvophyceae), brown (Phaeophyceae), and red (Rhodophyta) macroalgae, are primary producers in coastal ecosystems that fix carbon and release oxygen by photosynthesis, form diverse habitats, and provide food sources for various marine organisms, ranging from protists to vertebrates (Hurd et al., 2014). Although whether propagules of other green, brown, and red seaweeds are grazed by ciliates requires further investigation, propagule grazing by ciliates may be potentially widespread, which could explain the high propagule mortality rate. [Extracted from the article]

Aquaculture of the sea cucumber Apostichopus japonicus has emerged as a pivotal industry in northern China in the early 21st century. It is estimated that the cultivation area for this species spans 250,356 ha, yielding an annual production of 248,508 tons. The swift growth and intensification of sea cucumber farming practices have triggered a spectrum of diseases, resulting in significant economic detriment. This study offers an exhaustive account of a particular ciliate species, identified through smear and histopathological observations, hematoxylin-eosin staining, scanning electron microscopy, and molecular biology techniques, detailing its morphology, size, cellular architecture, and reproductive mode. The ciliate exhibits a torch-like shape, measuring 40–82 μm in length and 12–35 μm in width. It is characterized by the presence of both a macronucleus and a micronucleus. The anterior end is slender and blunt, while the posterior end is the widest part of the organism. A peristomal disc (PD) is situated at the body's terminus, with the mouth positioned centrally on the PD and a lip-like projection (6–10 μm in length) extending from one side. The organism's surface, particularly the area surrounding the oral region, is adorned with an abundance of long cilia. A single contractile vacuole is observable at the aboral end of the ciliate. It possesses 17–21 somatic kineties, complemented by 3 membranelles (M1, M2, M3) and a paroral membrane (PM) within the buccal cavity. One contractile vacuole was seen at the aboral end. There were 17–21 somatic kineties, while three membranes (M1, M2, M3) and a paroral membrane (PM) located within the buccal cavity. The first somatic kinety is notably more extended than the others, uniquely reaching a length of 10 μm around the PM. The PM, comprised of 2 somatic kineties in a "zig-zag" formation, follows a spiral path, making approximately 360-degree turns in conjunction with M1, M2, and M3, and culminates at the mouth depression. The ciliate reproduces through transverse binary fission or sexual conjugation. Based on these distinguishing features and molecular biological identification results, the ciliate is provisionally classified within the genus Boveria , as Boveria labialis. Histopathological examination has shown that these ciliates are predominantly found within the respiratory trees of their hosts, where they inflict damage to the epithelial tissues. This damage manifests as cell necrosis, structural disintegration, and the shedding of cells from the respiratory tree's epithelial lining. In severe cases, the affected respiratory tree and other viscera may be expelled. Epidemiological studies have indicated that infected individuals do not present with any overt external lesions. The findings of this research are instrumental for the management of diseases and the promotion of health within the sea cucumber aquaculture industry. • Displaying the oral apparatus structure of Boveria labialis by electron microscopy • Displaying the fine bodies structure after artificial depilation by electron microscopy • Artificial depilation provides an observational approach for other ciliates that grow cilia • After histopathological analysis, Boveria labialis parasitizes specifically in respiratory trees • A large number of ciliates can lead to necrosis, dropping, and thinning of the epithelial tissue [ABSTRACT FROM AUTHOR]

Sea urchins are primary herbivores on coral reefs, regulating algal biomass and facilitating coral settlement and growth. 1,2,3,4,5,6,7,8,9,10,11,12 Recurring mass mortality events (MMEs) of Diadema species Gray, 1825 have been recorded globally, 13,14,15,16,17,18,19,20,21,22,23 the most notorious and ecologically significant of which occurred in the Caribbean in 1983, 14,17,19,20 contributing to the shift from coral to algal-dominated ecosystems. 17,24,25 Recently, first evidence of Diadema setosum mass mortality was reported from the eastern Mediterranean Sea. 23 Here, we report extensive mass mortalities of several diadematoid species inhabiting the Red Sea and Western Indian Ocean (WIO) 26,27,28 including first evidence of mortalities in the genus Echinothrix Peters, 1853. Mortalities initiated in the Gulf of Aqaba on December 2022 and span the Red Sea, the Gulf of Oman, and the Western Indian Ocean (Réunion Island), with population declines reaching 100% at some sites. Infected individuals are characterized by spine loss and tissue necrosis, resulting in exposed skeletons (i.e., tests) and mortality. Molecular diagnostics of the 18S rRNA gene confirm the presence of a waterborne scuticociliate protozoan most closely related to Philaster apodigitiformis in infected specimens—identical to the pathogen found in the 2022 Caribbean mass mortality of Diadema antillarum. 13,15,18 Collapse of these key benthic grazers in the Red Sea and Western Indian Ocean may lead to algal dominance over corals, threatening the stability of coral reefs on a regional scale. 29,30,31,32 We issue a warning regarding the further expansion of mortalities and call for immediate monitoring and conservation efforts for these key ecological species. • Mass mortalities of diadematoid sea urchins spread through the Red Sea and WIO • Species of both Diadema and Echinothrix are susceptible to mortalities • Population declines in D. setosum and E. calamaris in the Gulf of Aqaba reach 100% • Molecular analyses confirm the presence of a Philaster -like scutocilliate protozoan Roth et al. report regional-scale mass mortalities of diadematoid sea urchins in the Red Sea and Western Indian Ocean, driving population declines of up to 100% in Diadema and Echinothrix species since December 2022. Genetic analyses confirm the presence of the Caribbean D. antillarum pathogen, a Philaster- like scuticociliate, in infected specimens. [ABSTRACT FROM AUTHOR]

The genus Pseudoblepharisma is currently comprised of only one species, P. tenue, and one variant, P. tenue var. viride, both described as free-living ciliates thriving in oxygen depleted freshwater habitats of Europe. Here we report on this genus being discovered from subtropical freshwaters of Florida, USA. The Florida strain diverges from the P. tenue by being much larger, as well as having a far higher density of intracellular symbiotic green algae, resembling P. tenue var. viride. Unlike its European counterparts, the North American strain was observed to build a lorica, likely useful for protection and feeding; this has not been previously described for this genus. In contrast to P. tenue, the Florida strain does not have endosymbiotic purple bacteria. Despite large distances between sampling zones, the species is a close match at a morphological level to Pseudoblepharisma tenue var. viride. We provide the first 18S rRNA gene sequence for this species, allowing future investigations into the biogeography of this genus. As intensive sampling efforts continue to increase, cryptic microbial species will continue to be recorded from diverse freshwater habitats at a global scale. [ABSTRACT FROM AUTHOR]

Background: Ciliated protists are a widely distributed, morphologically diverse, and genetically heterogeneous group of unicellular organisms, usually known for containing two types of nuclei: a transcribed polyploid macronucleus involved in gene expression and a silent diploid micronucleus responsible for transmission of genetic material during sexual reproduction and generation of the macronucleus. Although studies in a few species of culturable ciliated protists have revealed the highly dynamic nature of replicative and recombination events relating the micronucleus to the macronucleus, the broader understanding of the genomic diversity of ciliated protists, as well as their phylogenetic relationships and metabolic potential, has been hampered by the inability to culture numerous other species under laboratory conditions, as well as the presence of symbiotic bacteria and microalgae which provide a challenge for current sequencing technologies. Here, we optimized single-cell sequencing methods and associated data analyses, to effectively remove contamination by commensal bacteria, and generated high-quality genomes for a number of Euplotia species. Results: We obtained eight high-quality Euplotia genomes by using single-cell genome sequencing techniques. The genomes have high genomic completeness, with sizes between 68 and 125 M and gene numbers between 14K and 25K. Through comparative genomic analysis, we found that there are a large number of gene expansion events in Euplotia genomes, and these expansions are closely related to the phenotypic evolution and specific environmental adaptations of individual species. We further found four distinct subgroups in the genus Euplotes, which exhibited considerable genetic distance and relative lack of conserved genomic syntenies. Comparative genomic analyses of Uronychia and its relatives revealed significant gene expansion associated with the ciliary movement machinery, which may be related to the unique and strong swimming ability. Conclusions: We employed single-cell genomics to obtain eight ciliate genomes, characterized the underestimated genomic diversity of Euplotia, and determined the divergence time of representative species in this subclass for the first time. We also further investigated the extensive duplication events associated with speciation and environmental adaptation. This study provides a unique and valuable resource for understanding the evolutionary history and genetic diversity of ciliates. [ABSTRACT FROM AUTHOR]

Background: Ciliated protists are a widely distributed, morphologically diverse, and genetically heterogeneous group of unicellular organisms, usually known for containing two types of nuclei: a transcribed polyploid macronucleus involved in gene expression and a silent diploid micronucleus responsible for transmission of genetic material during sexual reproduction and generation of the macronucleus. Although studies in a few species of culturable ciliated protists have revealed the highly dynamic nature of replicative and recombination events relating the micronucleus to the macronucleus, the broader understanding of the genomic diversity of ciliated protists, as well as their phylogenetic relationships and metabolic potential, has been hampered by the inability to culture numerous other species under laboratory conditions, as well as the presence of symbiotic bacteria and microalgae which provide a challenge for current sequencing technologies. Here, we optimized single-cell sequencing methods and associated data analyses, to effectively remove contamination by commensal bacteria, and generated high-quality genomes for a number of Euplotia species. Results: We obtained eight high-quality Euplotia genomes by using single-cell genome sequencing techniques. The genomes have high genomic completeness, with sizes between 68 and 125 M and gene numbers between 14K and 25K. Through comparative genomic analysis, we found that there are a large number of gene expansion events in Euplotia genomes, and these expansions are closely related to the phenotypic evolution and specific environmental adaptations of individual species. We further found four distinct subgroups in the genus Euplotes, which exhibited considerable genetic distance and relative lack of conserved genomic syntenies. Comparative genomic analyses of Uronychia and its relatives revealed significant gene expansion associated with the ciliary movement machinery, which may be related to the unique and strong swimming ability. Conclusions: We employed single-cell genomics to obtain eight ciliate genomes, characterized the underestimated genomic diversity of Euplotia, and determined the divergence time of representative species in this subclass for the first time. We also further investigated the extensive duplication events associated with speciation and environmental adaptation. This study provides a unique and valuable resource for understanding the evolutionary history and genetic diversity of ciliates. [ABSTRACT FROM AUTHOR]

Magnetotactic bacteria(MTB) are a group of prokaryotes having the ability to orient and swim along geomagnetic fi eld lines because they contain intracellular magnetosomes that are synthesized through a biomineralization process. Magnetosomes have recently also been found in unicellular eukaryotes, which are referred to as magnetically responsive protists(MRPs). The magnetosomes have three origins in MRPs. In this study, we characterized a MTB-grazing ciliated MRP that was magnetically collected from intertidal sediment of Huiquan Bay, Qingdao, China. Based on 18S rRNA gene sequence analysis, the ciliated MRP was tentatively identifi ed as Uronemella parafi lificum HQ. Using transmission electron microscopy, we observed that magnetosomes having 2-3 shapes were randomly distributed within this ciliate. Energydispersive X-ray spectroscopy and high-resolution transmission electron microscopy images of the magnetosomes were consistent with them being composed of magnetite. Magnetosomes having the same shape and mineral composition were also detected in MTB that occurred in the same environment as the ciliated MRP. Statistical analysis showed that the size and shape of the magnetosomes in the ciliated MRP were similar to those in MTB. The results suggest that this ciliated MRP can graze, ingest, and digest various types of MTB. It is certainly worth noting that this is the fi rst record of MRPs in Asian aquatic sediment and suggesting they might be widely distributed. These results also support the assertion that MRPs probably contribute to the ecological cycles of iron, and expand possibilities for research into the mechanism of magnetoreception in eukaryotes. [ABSTRACT FROM AUTHOR]

SUMMARY Paramecium bursaria has hundreds of chlorella in the cell. These symbiotic chlorella cells supply maltose, a photosynthetic product, to the host. Only symbiotic chlorella retains the ability to release maltose to the extracellular space, whereas free‐living chlorella does not. To provide the host with maltose, a maltose transporter localized on the symbiotic chlorella plasma membrane is required. However, the molecular identity of the maltose transporter and its properties are unknown. To better understand the characteristics of the maltose transporter, we investigated how maltose release by Chlorella variabilis is affected by the excess external maltose and several agents that inhibit ATP synthesis or disrupt the ion gradient across cell membranes. Our overall findings, including the observation that C. variabilis did not utilize maltose in the growth medium, led to the conclusion that the maltose transporter is likely a unidirectional and active transporter, which utilizes a proton gradient across the plasma membrane and does not use ATP as its energy source. [ABSTRACT FROM AUTHOR]

We have assessed the effect of copepod chemical cues on the diel feeding rhythms of heterotrophic and mixotrophic marine protists. All phagotrophic protists studied exhibited relatively high diurnal feeding rates. The magnitude of the diel feeding rhythm, expressed as the quotient of day and night ingestion rates, was inversely related to the time that phagotrophic protists were maintained in the laboratory in an environment without predators. In the case of the recently isolated ciliate Strombidium arenicola, the rhythm was lost after a few months. When challenged with chemical alarm signals (copepodamides) from the copepod Calanus finmarchicus at realistic concentrations (0.6–6 pM), S. arenicola partially re-established diurnal feeding. Conversely, the amplitude of the diel feeding rhythm for the ciliate Mesodinium rubrum was not affected by copepodamides, although the 24-h integrated food intake increased by approximately 23%. For the dinoflagellates Gyrodinium dominans and Karlodinium armiger, copepodamides significantly reduced the amplitude of their diel feeding rhythms; significant positive effects on total daily ingestion were only observed in G. dominans. Finally, the dinoflagellate Oxyrrhis marina, isolated >20 years ago, showed inconsistent responses to copepodamides, except for an average 6% increase in its total ingestion over 24 h. Our results demonstrate that the predation risk by copepods affects the diel feeding rhythm of marine protists and suggests a species-specific response to predation threats. [ABSTRACT FROM AUTHOR]

The survival of all species requires appropriate behavioral responses to environmental challenges. Learning is one of the key processes to acquire information about the environment and adapt to changing and uncertain conditions. Learning has long been acknowledged in animals from invertebrates to vertebrates but remains a subject of debate in non-animal systems such a plants and single cell organisms. In this review I will attempt to answer the following question: are single cell organisms capable of learning? I will first briefly discuss the concept of learning and argue that the ability to acquire and store information through learning is pervasive and may be found in single cell organisms. Second, by focusing on habituation, the simplest form of learning, I will review a series of experiments showing that single cell organisms such as slime molds and ciliates display habituation and follow most of the criteria adopted by neuroscientists to define habituation. Then I will discuss disputed evidence suggesting that single cell organisms might also undergo more sophisticated forms of learning such as associative learning. Finally, I will stress out that the challenge for the future is less about whether or not to single cell organisms fulfill the definition of learning established from extensive studies in animal systems and more about acknowledging and understanding the range of behavioral plasticity exhibited by such fascinating organisms. • Single cell organisms are capable of learning. • Slime molds and ciliates display habituation, the simplest form of learning. • Evidence of associative learning in slime molds and ciliates are controversial. • More studies are needed to demonstrate that learning is pervasive in single cell organisms. [ABSTRACT FROM AUTHOR]

The germline-soma divide is a fundamental distinction in developmental biology, and different genes are expressed in germline and somatic cells throughout metazoan life cycles. Ciliates, a group of microbial eukaryotes, exhibit germline-somatic nuclear dimorphism within a single cell with two different genomes. The ciliate Oxytricha trifallax undergoes massive RNA-guided DNA elimination and genome rearrangement to produce a new somatic macronucleus (MAC) from a copy of the germline micronucleus (MIC). This process eliminates noncoding DNA sequences that interrupt genes and also deletes hundreds of germline-limited open reading frames (ORFs) that are transcribed during genome rearrangement. Here, we update the set of transcribed germline-limited ORFs (TGLOs) in O. trifallax. We show that TGLOs tend to be expressed during nuclear development and then are absent from the somatic MAC. We also demonstrate that exposure to synthetic RNA can reprogram TGLO retention in the somatic MAC and that TGLO retention leads to transcription outside the normal developmental program. These data suggest that TGLOs represent a group of developmentally regulated protein-coding sequences whose gene expression is terminated by DNA elimination. [ABSTRACT FROM AUTHOR]

We describe a new genus and species of blood‐dwelling apostome ciliate, Lynniagrapsolytica n. gen., n. sp. (Apostomatida: Colliniidae). A distinct kinety "hook" pattern on the tomite's posterior ventral face, coupled with its marine habitat and use of a decapod host, readily distinguishes this ciliate from all known colliniids. We detected the parasite in ~12% of Pachygrapsuscrassipes (Brachyura: Grapsidae) crabs in a California estuary and confirmed its presence at a Baja California rocky intertidal site. As existing methods failed to adequately stain this ciliate, we developed a new miniaturized silver carbonate impregnation staining method that produced excellent somatic and nuclear stains in all five observed cell types. A possibly unique trait is the active invagination of the tropho‐tomont's anterior to form a temporary "pseudocytopharynx," likely used for feeding. Histological examination revealed that the ciliate invaded and damaged skeletal muscle, the heart, connective tissues, and gonads. Survivorship analysis indicated that infected crabs experienced 2.6 times greater daily mortality than uninfected crabs. Laboratory and field experimental infection attempts failed, suggesting a complex life cycle with outside‐host development. Phylogenetic analysis at the 18S and COI loci confirmed the ciliate's placement in the Colliniidae. We emend the diagnosis of Family Colliniidae. [ABSTRACT FROM AUTHOR]

The mixotrophic dinoflagellate Tripos furca causes red tides in the waters of many countries. To understand its population dynamics, mortality due to predation as well as growth rate should be assessed. Prior to the present study, the heterotrophic dinoflagellates Noctiluca scintillans, Polykrikos kofoidii, Protoperidinium steinii, and mixotrophic dinoflagellate Fragilidium subglobosum were known to ingest T. furca. However, if other common heterotrophic protists are able to feed on T. furca has not been tested. We explored interactions between T. furca and nine heterotrophic dinoflagellates and one naked ciliate. Furthermore, we investigated the abundance of T. furca and common heterotrophic protists in coastal-offshore waters off Yeosu, southern Korea, on Jul 31, 2020, during its red tide. Among the tested heterotrophic protists, the heterotrophic dinoflagellates Aduncodinium glandula, Luciella masanensis, and Pfiesteria piscicida were able to feed on T. furca. However, the heterotrophic dinoflagellates Gyrodiniellum shiwhaense, Gyrodinium dominans, Gyrodinium jinhaense, Gyrodinium moestrupii, Oblea rotunda, Oxyrrhis marina, and the naked ciliate Rimostrombidium sp. were unable to feed on it. However, T. furca did not support the growth of A. glandula, L. masanensis, or P. piscicida. Red tides dominated by T. furca prevailed in the South Sea of Korea from Jun 30 to Sep 5, 2020. The maximum abundance of heterotrophic dinoflagellates in the waters off Yeosu on Jul 31, 2020, was as low as 5.0 cells mL-1, and A. glandula, L. masanensis, and P. piscicida were not detected. Furthermore, the abundances of the known predators F. subglobosum, N. scintillans, P. kofoidii, and Protoperidinium spp. were very low or negligible. Therefore, no or low abundance of effective predators might be partially responsible for the long duration of the T. furca red tides in the South Sea of Korea in 2020. [ABSTRACT FROM AUTHOR]

The endosymbiosis between Paramecium bursaria and Chlorella spp. is mutualistic. Symbiotic algae localize beneath the host Paramecium cell cortex compete for their attachment sites with preexisting organelle trichocysts. To examine the relationship between P. bursaria trichocysts and their symbiotic algae, algae-bearing or alga-free P. bursaria were starved for several days and the changes in the number of Chlorella sp. and presence or absence of trichocysts were evaluated. We conducted an indirect immunofluorescence microscopy with an anti-trichocyst monoclonal antibody against P. bursaria cells. Indirect immunofluorescence microscopy demonstrated that under starvation and darkness conditions, the immunofluorescence of trichocysts in alga-free P. bursaria decreased much faster than that in the normal algae-bearing P. bursaria. In the latter case, our observations proposed the possibility that the nutrition obtained from symbiotic algal digestion may promote trichocysts synthesis. This algal digestion mechanism may permit host P. bursaria cells to survive for a longer time under starvation condition. To the best of our knowledge, this may be a new benefit that host P. bursaria gain from harboring symbiotic algae. [ABSTRACT FROM AUTHOR]

Ciliates are single‐cell eukaryotes playing important roles in various ecosystems. Phylogenetic relationships within Hypotricha, one of the most polymorphic and highly derived ciliate groups, remain uncertain. Previous studies suggested that low genetic divergence might be the reason for poorly supported SSU rDNA tree topologies, despite the high morphological diversity of this group. In this study, we substantially increase the number of available hypotrich LSU rDNA gene sequences by the addition of 857 environmental sequences, and we investigate whether a more divergent gene and dense taxon sampling could better resolve the phylogeny of Hypotricha and shed light on the patterns of ecological transitions in the evolutionary history of the group. Pairwise distances of LSU rDNA sequences are generally higher than those for SSU rDNA within each order of Hypotricha, and both concatenated rDNA and LSU rDNA trees provide more resolution for hypotrich phylogenetics. Three traditional (morphology based) hypotrich orders, Stichotrichida, Sporadotrichida and Urostylida, are polyphyletic, but a monophyletic core Urostylida are found in our trees. A brackish/marine environment is inferred as ancestral within Hypotricha, with subsequent ecological diversification into freshwater, soil environments before the origin of major clades and some transitions back to the marine. However, inferred ecological transitions in Hypotricha are influenced by genes, methods and taxa. [ABSTRACT FROM AUTHOR]

Sex offers advantages even in primarily asexual species. Some ciliates appear to utilize such reproductive strategy with many mating types. However, the factors determining the composition of mating types in the unicellular ciliate Tetrahymena thermophila are poorly understood, and this is further complicated by non-Mendelian determination of mating type in the offspring. We therefore developed a novel population genetics model to predict how various factors influence the dynamics of mating type composition, including natural selection. The model predicted either the coexistence of all seven mating types or fixation of a single mating type in a population, depending on parameter combinations, irrespective of natural selection. To understand what factor(s) may be more influential and to test the validity of theoretical prediction, five replicate populations were maintained in laboratory such that several factors could be controlled or measured. Whole-genome sequencing was used to identify newly arising mutations and determine mating type composition. Strikingly, all populations were found to be driven by strong selection on newly arising beneficial mutations to fixation of their carrying mating types, and the trajectories of speed to fixation agreed well with our theoretical predictions. This study illustrates the evolutionary strategies that T. thermophila can utilize to optimize population fitness. [ABSTRACT FROM AUTHOR]

Background: Ciliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused genomes are extensively rearranged to generate functional minichromosomes. Interestingly, each ciliate species seems to have its way of processing genomes, providing a diversity of resources for studying genome plasticity and its regulation. Here, we sequenced and analyzed the macronuclear genome of different strains of Paramecium bursaria, a highly divergent species of the genus Paramecium which can stably establish endosymbioses with green algae. Results: We assembled a high-quality macronuclear genome of P. bursaria and further refined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that are potentially associated with endosymbiosis. Moreover, we observed an intensive chromosome breakage pattern that occurred during or shortly after sexual reproduction and contributed to highly variable gene dosage throughout the genome. However, patterns of copy number variation were highly correlated among genetically divergent strains, suggesting that copy number is adjusted by some regulatory mechanisms or natural selection. Further analysis showed that genes with low copy number variation among populations tended to function in basic cellular pathways, whereas highly variable genes were enriched in environmental response pathways. Conclusions: We report programmed DNA rearrangements in the P. bursaria macronuclear genome that allow cells to adjust gene copy number globally according to individual gene functions. Our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments. [ABSTRACT FROM AUTHOR]

We describe an inexpensive magnetic cell patterning method as a tool for protozoologists. The ciliate Vorticella convallaria is useful for various biofluidics applications. Here, we show that V. convallaria will ingest metal beads and that permanent magnets can be used to pattern cells in Petri dishes or a microfluidic device. Patterning is reversibly achieved by placing magnets at the point of desired cell attachment. Analogous magnetic manipulation could be performed using other phagocytic cells. [ABSTRACT FROM AUTHOR]

The host specificity of the recently described ciliate species Tetrahymena utriculariae was tested in a greenhouse growth experiment, which included 14 different species of aquatic Utricularia as potential host plants. We confirmed the high specificity of the interaction between U. reflexa and T. utriculariae, the former being the only tested host species able to maintain colonization for prolonged time periods. We conclude that this plant–microbe relationship is a unique and specialized form of digestive mutualism and the plant–microbe unit a suitable experimental system for future ecophysiological studies. [ABSTRACT FROM AUTHOR]

This paper is a first report on species of endosymbiotic ciliates (Litostomatea, Trichostomatia) inhabiting the intestine of zebras in South Africa. Ciliates from Mountain Zebra were investigated for the first time in the world. The wild population of mountain zebras in general and the Cape Mountain Zebra subspecies in particular is low in numbers: this species is included as vulnerable in the IUCN Red List. Approximately 15 species of trichostome ciliates from 9 different genera were found in the samples collected from wild zebras in Western Cape, South Africa. Some of the ciliate species are also common to horses and other equids, while others are unique for zebras. The ciliates of Triplumaria genus common to elephants and rhinoceroses, and the species Blepharosphaera ceratotherii previously described in rhinoceroses were found in equids for the first time. [ABSTRACT FROM AUTHOR]

Species belonging to the dinoflagellate genus Prorocentrum are known to cause red tides or harmful algal blooms. To understand the dynamics of a Prorocentrum sp., its growth and mortality due to predation need to be assessed. However, there are only a few Prorocentrum spp. for which heterotrophic protist predators have been reported. We explored feeding by the common heterotrophic dinoflagellates Gyrodinium dominans, Oxyrrhis marina, Pfiesteria piscicida, Oblea rotunda, and Polykrikos kofoidii and the naked ciliate Strombidinopsis sp. (approx. 90 µm cell length) on the planktonic species Prorocentrum triestinum, P. cordatum, P. donghaiense, P. rhathymum, and P. micans as well as the benthic species P. lima and P. hoffmannianum. All heterotrophic protists tested were able to feed on the planktonic prey species. However, O. marina and O. rotunda did not feed on P. lima and P. hoffmannianum, while G. dominans, P. kofoidii, and Strombidinopsis sp. did. The growth and ingestion rates of G. dominans and P. kofoidii on one of the seven Prorocentrum spp. were significantly different from those on other prey species. G. dominans showed the top three highest growth rates when it fed on P. triestinum, P. cordatum, and P. donghaiense, however, P. kofoidii had negative growth rates when fed on these three prey species. In contrast, P. kofoidii had a positive growth rate only when fed on P. hoffmannianum. This differential feeding on Prorocentrum spp. between G. dominans and P. kofoidii may provide different ecological niches and reduce competition between these two common heterotrophic protist predators. [ABSTRACT FROM AUTHOR]

The ciliate Tetrahymena thermophila does not require sterols for growth and synthesizes pentacyclic triterpenoid alcohols, mainly tetrahymanol, as sterol surrogates. However, when sterols are present in the environment, T. thermophila efficiently incorporates and modifies them. These modifications consist of desaturation reactions at positions C5(6), C7(8), and C22(23), and de‐ethylation at C24 of 29‐carbon sterols (i.e. phytosterols). Three out of four of the enzymes involved in the sterol modification pathway have been previously identified. However, identification of the sterol C22 desaturase remained elusive, as did other basic aspects of this metabolism. To get more insights into this peculiar metabolism, we here perform a whole transcriptome analysis of T. thermophila in response to exogenous cholesterol. We found 356 T. thermophila genes to be differentially expressed after supplementation with cholesterol for 2 h. Among those that were upregulated, we found two genes belonging to the long spacing family of desaturases that we tentatively identified by RNAi analysis as sterol C22 desaturases. Additionally, we determined that the inhibition of tetrahymanol synthesis after supplementation with cholesterol occurs by a transcriptional downregulation of genes involved in squalene synthesis and cyclization. Finally, we identified several uncharacterized genes that are likely involved in sterols transport and signaling. [ABSTRACT FROM AUTHOR]

In endolysosomal networks, two hetero-hexameric tethers called HOPS and CORVET are found widely throughout eukaryotes. The unicellular ciliate Tetrahymena thermophila possesses elaborate endolysosomal structures, but curiously both it and related protozoa lack the HOPS tether and several other trafficking proteins, while retaining the related CORVET complex. Here, we show that Tetrahymena encodes multiple paralogs of most CORVET subunits, which assemble into six distinct complexes. Each complex has a unique subunit composition and, significantly, shows unique localization, indicating participation in distinct pathways. One pair of complexes differ by a single subunit (Vps8), but have late endosomal versus recycling endosome locations. While Vps8 subunits are thus prime determinants for targeting and functional specificity, determinants exist on all subunits except Vps11. This unprecedented expansion and diversification of CORVET provides a potent example of tether flexibility, and illustrates how 'backfilling' following secondary losses of trafficking genes can provide a mechanism for evolution of new pathways. [ABSTRACT FROM AUTHOR]

The pelagic / anoxic hypolimnion population of Spirostomum teres was investigated as a part of the long-term ciliates' monitoring (2003-2016) in an oligo- to mesotrophic monomictic hyposaline crater lake Alchichica (Puebla / Veracruz, Mexico), including an analysis of picoplankton (both heterotrophic, HPP and autotrophic, APP) and inorganic compounds of nitrogen (ammonium, nitrite, nitrate), phosphorus (dissolved reactive phosphorus, DRP) and silicon. Additionally, detailed studies of the ciliate vertical distribution and feeding activity measured upon fluorescently labelled APP (picocyanobacteria) were carried out. The results were compared with those from a neighbour freshwater crater lake La Preciosa and with a meromictic karstic lake La Cruz (Cuenca, Spain). The ciliate vertical distribution within the water column was very well defined: During the first decade, the benthic population was frequently found throughout a developing stratification of the lake. The established stratification of the lake turned the conditions favourable for the formation of an oxycline / hypolimnion population, typically, several meters below the deep chlorophyll maximum (formed basically by diatoms); the population preferred the layers without detectable dissolved oxygen. However, an observed gradient of light (PAR) could support both oxygenic and anoxygenic photosynthesis. Late stratification after deepening of the thermocline reduced the layers with S. teres population to a minimum apparently due to the drastic change in physicochemical conditions within a metalimnion, coupled with an oxycline, and limited to 1 to 2 meters; microstratification was found. Last years, the very bottom population disappeared or it was reduced and the late stratification S. teres peaks were smaller or did not appeared. Generally, S. teres oxycline / anoxic hypolimnion population was observed from June through November. Optimum picoplankton numbers in conditions that supported the ciliate growth were found: The ciliate was peaking at APP of 0.6 to 1 × 105 cells mL-1; the optimum of HPP was observed round 1.4 × 106 cells mL-1. S. teres was efficiently feeding upon picocyanobacteria in numbers of 105 cells mL-1 reaching the clearance rate of 2000 nL cell-1h-1, which represented in average 130 to 210 cells cell-1h-1 ingested. Feeding upon purple sulphur bacteria was observed but only during the end of the lake stable stratification when the ciliate population was already dropping. On the other hand, the volume specific clearance of S. teres upon picocyanobacteria (103 h-1) did not support the hypothesis that they could serve as a sole prey. Feeding upon eukaryote phytoplankton (chlorophytes Monoraphidium minutum, diatoms Cyclotella choctawhatcheeana) could be of higher importance that previously supposed. Additionally, a use of ingested and retained photosynthetic prokaryotes is hypothesized. [ABSTRACT FROM AUTHOR]

The ciliate Euplotes deviates from the universal genetic code by translating UGA as cysteine and using UAA and UAG as the termination codon. Here, we cloned and sequenced the Cathepsin B gene of Euplotes octocarinatus (Eo‐CTSB) which containing several in‐frame stop codons throughout the coding sequence. We provide evidences, based on 3′‐RACE method and Western blot, that the Eo‐CTSB gene is actively expressed. Comparison of the derived amino acid sequence with the homologs in other eukaryotes revealed that UAA and UAG may code for glutamine in Eo‐CTSB. These findings imply an evolutionary complexity of stop codon reassignment in eukaryotes. [ABSTRACT FROM AUTHOR]

Background: Whole-genome shotgun sequencing, which stitches together millions of short sequencing reads into a single genome, ushered in the era of modern genomics and led to a rapid expansion of the number of genome sequences available. Nevertheless, assembly of short reads remains difficult, resulting in fragmented genome sequences. Ultimately, only a sequencing technology capable of capturing complete chromosomes in a single run could resolve all ambiguities. Even "third generation" sequencing technologies produce reads far shorter than most eukaryotic chromosomes. However, the ciliate Oxytricha trifallax has a somatic genome with thousands of chromosomes averaging only 3.2 kbp, making it an ideal candidate for exploring the benefits of sequencing whole chromosomes without assembly. Results: We used single-molecule real-time sequencing to capture thousands of complete chromosomes in single reads and to update the published Oxytricha trifallax JRB310 genome assembly. In this version, over 50% of the completed chromosomes with two telomeres derive from single reads. The improved assembly includes over 12,000 new chromosome isoforms, and demonstrates that somatic chromosomes derive from variable rearrangements between somatic segments encoded up to 191,000 base pairs away. However, while long reads reduce the need for assembly, a hybrid approach that supplements long-read sequencing with short reads for error correction produced the most complete and accurate assembly, overall. Conclusions: This assembly provides the first example of complete eukaryotic chromosomes captured by single sequencing reads and demonstrates that traditional approaches to genome assembly can mask considerable structural variation. [ABSTRACT FROM AUTHOR]

Diverse animal species exhibit highly stereotyped behavioral actions and locomotor sequences as they explore their natural environments. In many such cases, the neural basis of behavior is well established, where dedicated neural circuitry contributes to the initiation and regulation of certain response sequences. At the microscopic scale, single-celled eukaryotes (protists) also exhibit remarkably complex behaviors and yet are completely devoid of nervous systems. Here, to address the question of how single cells control behavior, we study locomotor patterning in the exemplary hypotrich ciliate Euplotes , a highly polarized cell, which actuates a large number of leg-like appendages called cirri (each a bundle of ∼25–50 cilia) to swim in fluids or walk on surfaces. As it navigates its surroundings, a walking Euplotes cell is routinely observed to perform side-stepping reactions, one of the most sophisticated maneuvers ever observed in a single-celled organism. These are spontaneous and stereotyped reorientation events involving a transient and fast backward motion followed by a turn. Combining high-speed imaging with simultaneous time-resolved electrophysiological recordings, we show that this complex coordinated motion sequence is tightly regulated by rapid membrane depolarization events, which orchestrate the activity of different cirri on the cell. Using machine learning and computer vision methods, we map detailed measurements of cirri dynamics to the cell's membrane bioelectrical activity, revealing a differential response in the front and back cirri. We integrate these measurements with a minimal model to understand how Euplotes —a unicellular organism—manipulates its membrane potential to achieve real-time control over its motor apparatus. [Display omitted] • Euplotes uses bundles of cilia (cirri) on its ventral surface to walk and swim • Forward movement is interrupted by highly coordinated turning maneuvers • Membrane depolarizations trigger turning with distinct cirri behaving differently • A minimal mechanical model maps cirri dynamics to locomotor gait Laeverenz-Schlogelhofer et al. combine high-speed imaging with simultaneous electrophysiological recordings in Euplotes , a single cell with leg-like appendages (cirri), to show how the cell's membrane potential coordinates cirri movement and dynamic transitions between whole-cell walking or turning. [ABSTRACT FROM AUTHOR]