Comparative before-after study of fever prevention versus targeted temperature management following out-of-hospital cardiac arrest

Background

International guidelines for neuroprotection following out-of-hospital cardiac arrest (OHCA) recommend fever prevention ahead of routine temperature management. This study aimed to identify any effect of changing from targeted temperature management to fever prevention on neurological outcome following OHCA.

Methods

A retrospective observational cohort study was conducted of consecutive admissions to an ICU at a tertiary OHCA centre. Comparison was made between a period of protocolised targeted temperature management (TTM) to 36 °C and a period of fever prevention.

Results

Data were available for 183 patients. Active temperature management was administered in 86/118 (72%) of the TTM cohort and 20/65 (31%) of the fever prevention group. The median highest temperature prior to the start of temperature management was significantly lower in the TTM group at 35.6 (IQR 34.9-36.2) compared to 37.9 °C (IQR 37.7-38.2) in the fever prevention group (adjusted p < 0.001).There was no difference in the proportion of patients discharged with Cerebral Performance Category 1 or 2 between the groups (42% vs. 40%, p = 0.88). Patients in the fever prevention group required a reduced duration of noradrenaline (36 vs. 46 h, p = 0.03) and a trend towards a reduced duration of propofol (37 vs. 56 h, p = 0.06).In unadjusted analysis, use of active temperature management (irrespective of group) appeared to be associated with decreased risk of poor outcome (OR = 0.43, 95% CI 0.23-0.78) but after adjustment for patient age, presenting rhythm, witnessed arrest and duration of CPR, this was no longer significant (OR = 0.93, 95% CI 0.37-2.31, p = 0.88).

Conclusion

Switching from TTM to fever prevention following OHCA was associated with similar rates of neurological outcomes, with a possible decrease in sedation and vasopressor requirements.

Quantifying hospital environmental ventilation using carbon dioxide monitoring - a multicentre study

The COVID-19 pandemic has highlighted the importance of environmental ventilation in reducing airborne pathogen transmission. Carbon dioxide monitoring is recommended in the community to ensure adequate ventilation. Dynamic measurements of ventilation quantifying human exhaled waste gas accumulation are not conducted routinely in hospitals. Instead, environmental ventilation is allocated using static hourly air change rates. These vary according to the degree of perceived hazard, with the highest change rates reserved for locations where aerosol-generating procedures are performed, where medical/anaesthetic gases are used and where a small number of high-risk infective or immunocompromised patients may be isolated to reduce cross-infection. We aimed to quantify the quality and distribution of ventilation in hospital by measuring carbon dioxide levels in a two-phased prospective observational study. First, under controlled conditions, we validated our method and the relationship between human occupancy, ventilation and carbon dioxide levels using non-dispersive infrared carbon dioxide monitors. We then assessed ventilation quality in patient-occupied (clinical) and staff break and office (non-clinical) areas across two hospitals in Scotland. We selected acute medical and respiratory wards in which patients with COVID-19 are cared for routinely, as well as ICUs and operating theatres where aerosol-generating procedures  are performed routinely. Between November and December 2022, 127,680 carbon dioxide measurements were obtained across 32 areas over 8 weeks. Carbon dioxide levels breached the 800 ppm threshold for 14% of the time in non-clinical areas vs. 7% in clinical areas (p < 0.001). In non-clinical areas, carbon dioxide levels were > 800 ppm for 20% of the time in both ICUs and wards, vs. 1% in operating theatres (p < 0.001). In clinical areas, carbon dioxide was > 800 ppm for 16% of the time in wards, vs. 0% in ICUs and operating theatres (p < 0.001). We conclude that staff break, office and clinical areas on acute medical and respiratory wards frequently had inadequate ventilation, potentially increasing the risks of airborne pathogen transmission to staff and patients. Conversely, ventilation was consistently high in the ICU and operating theatre clinical environments. Carbon dioxide monitoring could be used to measure and guide improvements in hospital ventilation.

Prostatic stromal tumour of uncertain malignant potential treated with robotic-assisted radical prostatectomy: medium-term oncological and functional outcome of two cases

Stromal tumour of uncertain malignant potential (STUMP) is a rare tumour of the prostate with variable and unpredictable risk and clinical progression. There is no clear consensus on how it should be managed. We describe two cases of patients who presented to their general practitioners with raised prostate-specific antigen in one instance and an abnormal digital rectal examination in the other. Biopsies were carried out and a diagnosis of STUMP was made. Both cases were managed with robot-assisted radical prostatectomy and after 4.8 years of follow-up, there has not been any recurrence. This is the first reported UK case in which STUMP has been successfully managed with robotic surgery with excellent medium-term results. Radical prostatectomy can be used to treat STUMP tumour with good oncological and functional outcomes.

Exploring Microeukaryote Community Characteristics and Niche Differentiation in Arid Farmland Soil at the Northeastern Edge of the Tibetan Plateau

The northeastern edge of the Tibetan Plateau exhibits diverse climate and landform variations, and has experienced substantial recent environmental changes, which may significantly impact local agricultural practices. Understanding the microeukaryote community structure within agricultural soils is crucial for finding out the biological responses to such changes and may guide future agricultural practices. In this study, we employed high-throughput amplicon sequencing to examine 29 agricultural soil samples from seven research areas around the northeastern edge of the Tibetan Plateau. The findings revealed that the predominant biological communities in these soils were characterized by a high abundance of Alveolata, Amoebozoa, and Rhizaria. Ascomycota displayed the highest relative abundance among fungal communities. Moreover, notable distinctions in microeukaryote community composition were observed among the study sites. Co-occurrence network analysis highlighted interactions between the biological communities. Furthermore, our results elucidated that deterministic and stochastic processes exerted diverse influences on the distribution of protozoan and fungal communities. This study provides valuable insight into the microeukaryote structure in the agricultural soils of the northeastern edge of the Tibetan Plateau, shedding light on the intricate relationships between environmental factors, microeukaryote communities, and agricultural productivity.

On four epibiotic peritrichous ciliates (Protozoa, Ciliophora) found in Lake Weishan Wetland: morphological and molecular data support the establishment of a new genus, Parapiosoma gen. nov., and two new species

During a study on the diversity of ciliated protists in Lake Weishan Wetland, the largest wetland in northern China, four epibiotic sessilid peritrichs were isolated from aquatic host animals. Two of them, i.e., Epistylis cambari Kellicott, 1885 and Epistylis lwoffi Fauré-Fremiet, 1943, were known species whereas the other two, i.e., Parapiosoma typicum gen. nov., sp. nov. and Orborhabdostyla gracilis sp. nov., are new to science. The new genus Parapiosoma gen. nov. is characterized by its branched non-contractile stalk, everted peristomial lip, obconical macronucleus and transverse silverlines. Two species are assigned to the new genus, namely Parapiosoma typicum sp. nov. and Parapiosoma gasterostei (Fauré-Fremiet, 1905) comb. nov. Morphologically, P. typicum sp. nov. is recognized by its goblet-shaped zooids, single-layered peristomial lip, dichotomously branched stalk, and infundibular polykinety 3 (P3) containing three equal-length rows. Orborhabdostyla gracilis sp. nov. is characterized by its slender zooid, curved macronucleus, and three equal-length rows in infundibular P3. Improved diagnoses and redescriptions of E. cambari and E. lwoffi are provided including, for the first time, data on the ciliature of E. cambari. Phylogenetic analyses based on SSU rDNA, ITS1-5.8S rDNA -ITS2, and LSU rDNA sequence data strongly support the assertion that the family Epistylididae comprises morphospecies with different evolutionary lineages and indicate that Parapiosoma gen. nov. may represent a new taxon at family level.

Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa

Ciliated protozoa (ciliates) are unicellular eukaryotes, several of which are important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome of ciliates can promote a better understanding of the genetic mode and evolutionary history of these organisms and help optimize codons to improve gene editing efficiency in model ciliates. In this study, the following indices were calculated: the guanine-cytosine (GC) content, the frequency of the nucleotides at the third position of codons (T3, C3, A3, G3), the effective number of codons (ENc), GC content at the 3rd position of synonymous codons (GC3s), and the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, Neutrality plot analysis, ENc plot analysis, and correlation analysis were employed to explore the main influencing factors of CUB. The results showed that the GC content in the MAC genomes of each of 21 ciliate species, the genomes of which were relatively complete, was lower than 50%, and the base compositions of GC and GC3s were markedly distinct. Synonymous codon analysis revealed that the codons in most of the 21 ciliates ended with A or T and four codons were the general putative optimal codons. Collectively, our results indicated that most of the ciliates investigated preferred using the codons with anof AT-ending and that codon usage bias was affected by gene mutation and natural selection.

Comparative transcriptome and antioxidant biomarker response reveal molecular mechanisms to cope with zinc ion exposure in the unicellular eukaryote Paramecium

The development of industry has resulted in excessive environmental zinc exposure which has caused various health problems in a wide range of organisms including humans. The mechanisms by which aquatic microorganisms respond to environmental zinc stress are still poorly understood. Paramecium, a well-known ciliated protozoan and a popular cell model in heavy metal stress response studies, was chosen as the test unicellular eukaryotic organism in the present research. In this work, Paramecium cf. multimicronucleatum cells were exposed in different levels of zinc ion (0.1 and 1.0 mg/L) for different periods of exposure (1 and 4 days), and then analyzed population growth, transcriptomic profiles and physiological changes in antioxidant enzymes to explore the toxicity and detoxification mechanisms during the zinc stress response. Results demonstrated that long-term zinc exposure could have restrained population growth in ciliates, however, the response mechanism to zinc exposure in ciliates is likely to show a dosage-dependent and time-dependent manner. The differentially expressed genes (DEGs) were identified the characters by high-throughput sequencing, which remarkably enriched in the phagosome, indicating that the phagosome pathway might mediate the uptake of zinc, while the pathways of ABC transporters and Na⁺/K⁺-transporting ATPase contributed to the efflux transport of excessive zinc ions and the maintenance of osmotic balance, respectively. The accumulation of zinc ions triggered a series of adverse effects, including damage to DNA and proteins, disturbance of mitochondrial function, and oxidative stress. In addition, we found that gene expression changed significantly for metal ion binding, energy metabolism, and oxidation-reduction processes. RT-qPCR of ten genes involved in important biological functions further validated the results of the transcriptome analysis. We also continuously monitored changes in activity of four antioxidant enzymes (SOD, CAT, POD and GSH-PX), all of which peaked on day 4 in cells subjected to zinc stress. Collectively, our results indicate that excessive environmental zinc exposure initially causes damage to cellular structure and function and then initiates detoxification mechanisms to maintain homeostasis in P. cf. multimicronucleatum cells.

Comparative genomics provides insights into the phylogeny and environmental adaptations of Peritrichia (Protista, Ciliophora) - a potential resource for environmental pollution control and bioremediation

Peritrichs are one of the largest groups within the class Oligohymenophorea. They have a worldwide distribution and a high degree of species diversity. Using the single-cell genome sequencing technique, we obtained the genomes of five sessilid peritrichs. Combining both genomic and transcriptomic data of other publicly available oligohymenophorean ciliates (including the genomes of three sessilid peritrichs from our team's previous study), we conducted a comparative genomics study. Our phylogenomic analyses using both maximum likelihood and Bayesian inference methods recovered the subclass Peritrichia and each of its two orders (Sessilida and Mobilida) as being monophyletic. The non-monophyly of two families (Vorticellidae and Zoothamniidae) was also well supported in both trees. Molecular clock analysis showed that the origin of the subclass Peritrichia was estimated to be during the late Proterozoic. We also analyzed the stop codon usage of 44 oligohymenophoreans. The results showed that most of these species used TGA as the biased stop codon and reassigned the other two stop codons (TAA and TAG) to code amino acids. In addition, we found that the presence of a typical peritrich lorica is a plesiomorphic character of the family Vaginicolidae. Through GO enrichment analysis for group-specific orthogroups of Vaginicolidae, we successfully identified the biological process and molecular function GO terms that were linked with the typical peritrich lorica, including three glycosaminoglycan-related and two chitin-related GO terms. Finally, our enrichment analyses of significantly expanded gene families in Peritrichia found that sessilids were more tolerant to environmental stress (mainly organic matter) than mobilids, suggesting that peritrich lineages (especially sessilids) may have the potential for application in environmental pollution control and bioremediation. Together, the results presented in this study will facilitate wider genome-scale phylogenetic analyses of Peritrichia and deepen the understanding of their unique advantages for environmental pollution control bioremediation.

Antibiotic nitrofurazone drives the functional dynamics of periphytic protozoan fauna in marine environments

The use of functional traits of a community as a method to measure its functional dynamics in response to environmental change has gained attention because trait-based approaches offer systematic opportunities to understand the interactions between species diversity and ecosystem function. However, the relationship between functional traits of periphytic protozoa and contamination of aquatic habitats with antibiotics is poorly understood. In this study, we investigated the influence of the antibiotic nitrofurazone on functional traits of marine periphytic protozoan fauna. For this purpose, the protozoan assemblages were collected from coastal waters of the Yellow Sea at Qingdao, northern China, during four seasons of a one-year cycle using glass microscope slides as artificial substrates. The test protozoan communities were then exposed to various treatments of nitrofurazone in laboratory bioassay experiments. Our results demonstrated that the modalities of the functional traits of protozoan communities were generally driven by nitrofurazone toxicity. Briefly, R-mode linked to Q-mode (RLQ) and fourth-corner analyses revealed strong positive correlations between functional traits and nitrofurazone treatments. Trait syndromes in terms of body length, width, weight, height, and size to volume ratios were significantly influenced by nitrofurazone exposure. In particular, small and medium body size species of different feeding types, i.e., algivores, bacterivores, raptors or non-selectives, were more sensitive than other protozoan species to higher concentrations of nitrofurazone. Our findings demonstrate that antibiotic toxicity is likely to affect periphytic protozoan community function, shape the functional processes, and induce toxic responses in the community. The findings of this study suggest that periphytic protozoan communities and their functional traits are suitable bioindicators for evaluating the ecotoxicity of nitrofurazone in marine environments.

Potential role of N6-adenine DNA methylation in alternative splicing and endosymbiosis in Paramecium bursaria

N⁶-adenine DNA methylation (6mA), a rediscovered epigenetic mark in eukaryotic organisms, diversifies in abundance, distribution, and function across species, necessitating its study in more taxa. Paramecium bursaria is a typical model organism with endosymbiotic algae of the species Chlorella variabilis. This consortium therefore serves as a valuable system to investigate the functional role of 6mA in endosymbiosis, as well as the evolutionary importance of 6mA among eukaryotes. In this study, we report the first genome-wide, base pair-resolution map of 6mA in P. bursaria and identify its methyltransferase PbAMT1. Functionally, 6mA exhibits a bimodal distribution at the 5' end of RNA polymerase II-transcribed genes and possibly participates in transcription by facilitating alternative splicing. Evolutionarily, 6mA co-evolves with gene age and likely serves as a reverse mark of endosymbiosis-related genes. Our results offer new insights for the functional diversification of 6mA in eukaryotes as an important epigenetic mark.

From oral structure to molecular evidence: new insights into the evolutionary phylogeny of the ciliate order Sessilida (Protista, Ciliophora), with the establishment of two new families and new contributions to the poorly studied family Vaginicolidae

Ciliated protists represent one of the most primitive and diverse lineages of eukaryotes, with nuclear dimorphism, a distinctive sexual process (conjugation), and extensive genome rearrangements. Among divergent ciliate lineages, the peritrich order Sessilida includes members with a colonial lifestyle, which may hint to an independent evolutionary attempt for multicellularity, although they are still single-celled organisms. To date, the evolution and phylogeny of this group are still far from clear, in part due to the paucity of molecular and/or morphological data for many taxa. In this study, we extend taxon sampling of a loricate group of sessilids by obtaining 69 new rDNA (SSU rDNA, ITS1-5.8S rDNA-ITS2, and LSU rDNA) sequences from 20 well-characterized representative species and analyze the phylogenetic relationships within Sessilida. The main findings are: (i) the genera Rhabdostyla and Campanella each represents a unique taxon at family level, supporting the establishment of two new families, i.e., Rhabdostylidae n. fam. and Campanellidae n. fam., respectively, the former being sister to a morphologically heterogeneous clade comprising Astylozoidae and several incertae sedis species and the latter occupying the basal position within the Sessilida clade; (ii) the structure of infundibular polykinety 3 is likely to be a phylogenetically informative character for resolving evolutionary relationships among sessilids; (iii) differences between sparsely and the densely arranged silverline systems could be a suprageneric taxonomic character; (iv) the monophyly of Vaginicolidae is confirmed, which is consistent with its specialized morphology, i.e., the possession of a typical peritrich lorica which might be an apomorphy for this group; (v) within Vaginicolidae, the monotypic Cothurniopsis sensu Stokes, 1893 is a synonym of Cothurnia Ehrenberg, 1831, and a new combination is created, i.e., Cothurnia valvata nov. comb.; (vi) Vaginicola sensu lato comprises at least two distinctly divergent clades, one affiliated with Thuricola and the other with a systematically puzzling clade represented by Vaginicola tincta.

Large-scale phylogenetic analysis provides insights into the diversification and evolution of sessilid peritrich ciliates (Protista: Ciliophora)

The Peritrichia is a speciose and morphologically distinctive assemblage of ciliated protists that was first observed by Antonie van Leeuwenhoek over 340 years ago. In the last two decades, the phylogenetic relationships of this group have been increasingly debated as morphological and molecular analyses have generated contrasting conclusions, mainly owing to limited sampling. In the present study, we performed expanded phylogenetic analyses of 152 sessilid peritrichs collected from 14 different provinces of China and 141 SSU rDNA peritrich sequences from GenBank. The results of the analyses revealed new divergent relationships between and within major clades that challenge the morphological classification of this group including, (1) the recovery of four major phylogenetically divergent clades in the monophyletic order Sessilida, (2) aboral structures such as the stalk and spasmoneme were evolutionary labile, (3) the stalk or/and spasmoneme was lost in each divergent clade indicating that parallel evolution occurred in sessilid peritrichs and (4) the life cycle and habit drive the diversity of aboral structures as well as diversification and evolution in peritrichs.

Giant proteins in a giant cell: Molecular basis of ultrafast Ca2+-dependent cell contraction

The giant single-celled eukaryote, Spirostomum, exhibits one of the fastest movements in the biological world. This ultrafast contraction is dependent on Ca²⁺ rather than ATP and therefore differs to the actin-myosin system in muscle. We obtained the high-quality genome of Spirostomum minus from which we identified the key molecular components of its contractile apparatus, including two major Ca²⁺ binding proteins (Spasmin 1 and 2) and two giant proteins (GSBP1 and GSBP2), which act as the backbone and allow for the binding of hundreds of spasmins. The evidence suggests that the GSBP-spasmin protein complex is the functional unit of the mesh-like contractile fibrillar system, which, coupled with various other subcellular structures, provides the mechanism for repetitive ultrafast cell contraction and extension. These findings improve our understanding of the Ca²⁺-dependent ultrafast movement and provide a blueprint for future biomimicry, design, and construction of this kind of micromachine.

Predation risk affects the ecotoxicity evaluation of antibiotics: Population growth and antioxidase activity in the ciliate Paramecium jenningsi

Although predation risk exists under natural conditions, its role is usually ignored when evaluating the ecotoxicity of environmental contaminants, and the interaction between predation risk and antibiotic ecotoxicity is not yet clear. To investigate the nonconsumptive effects (NCEs) of predation on the ecotoxicity evaluation of antibiotics, the median lethal concentration (LC₅₀), relative population growth rate (RGR), and activities of three antioxidases were measured in the ciliate Paramecium jenningsi exposed to graded concentrations of the antibiotics nitrofurazone (NFZ) or erythromycin (ERY) in the presence or absence of a predator, i.e., the ciliate Didinium nasutum. The results showed that (1) NCEs significantly reduced the LC₅₀ of NFZ but had no effect on that of ERY; (2) predation pressure alone had no significant effect on the inhibitory rate of the P. jenningsi population, but the interaction with NFZ was synergistic, while that with CRY was additive; (3) the concentrationresponse (i.e., mortality) model for each antibiotic exposure with and without predation pressure differed significantly in the parameter slope; (4) RGRs were significantly reduced by antibiotic exposure or NCEs; only in NFZ-exposed groups did the RGRs decrease linearly with increasing exposure concentration; and (5) the activities of all three antioxidases significantly increased due to NCEs or following exposure to antibiotics. In brief, NCEs were detected in P. jenningsi, and these had additive or synergistic effects on antibiotic ecotoxicity, but their magnitude depended on the properties and exposure concentrations of the antibiotics. Our findings suggest that it is necessary to consider the roles of NCEs in the ecotoxicity evaluation of environmental contaminants.

New contributions to the Cyrtophoria ciliates (Protista, Ciliophora): Establishment of new taxa and phylogenetic analyses using two ribosomal genes

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.

New considerations on the phylogeny of Sessilida (Protista: Ciliophora: Peritrichia) based on multiple-gene information, with emphasis on colonial taxa

The subclass Peritrichia, containing two orders Sessilida and Mobilida, is a major group of ciliates with worldwide distribution and high species diversity. Several studies have investigated the phylogeny of peritrichs; however, the evolutionary relationships and classification of some families and genera within the Sessilida remain unclear. In the present study, we isolated and identified 22 peritrich populations representing four families and six genera and obtained 64 rDNA sequences to perform phylogenetic analyses and assess their systematic relationships. Ancestral character reconstruction was also carried out to infer evolutionary routes within the Sessilida. The results indicate: (1) family Vaginicolidae is monophyletic and acquisition of the typical peritrich lorica represents a single evolutionary divergence; (2) core epistylidids evolved from a Zoothamnium-like ancestor and experienced spasmoneme loss during evolution; (3) Campanella clusters with species in the basal clade and shows stable morphological differences with other epistylidids, supporting its assignment to a separate family; (4) the structure of the peristomial lip may be a genus-level character rather than a diagnostic character for discriminating Epistylididae and Operculariidae, thus a redefinition of Operculariidae should be carried out when more species have been investigated; (5) some characters, such as lifestyle (solitary or colonial), spasmoneme and living habit (sessile or free-swimming), evolved repeatedly among sessilids indicating that species with non-contractile stalks or that are free-swimming have multiple evolutionary routes and might derive from any sessilid lineage without a lorica. The close phylogenetic relationships of some morphologically distinct sessilids imply that the diagnoses of some genera and families should be improved.

Phylogeny of the anaerobic ciliate genus Sonderia (Protista: Ciliophora: Plagiopylea), including the description of three novel species and a brief revision of the genus

Anaerobic protists in general, and ciliates in particular, are important components of anoxic or hypoxic environments, however, their diversity remains underestimated. Sonderia is a poorly studied genus that is distributed worldwide and is commonly found in anaerobic environments. In the present study, the taxonomy and phylogeny of three new species, namely Sonderia aposinuata sp. nov., Sonderia paramacrochilus sp. nov. and Sonderia steini sp. nov., collected from China, were investigated based on microscopic observations and SSU rRNA gene sequencing methods. Sonderia aposinuata sp. nov. is diagnosed mainly by having a relatively large body size, a crescent-shaped oral opening, numerous slender extrusomes, one suture on the ventral side and two on the dorsal side, and a buccal cavity that occupies the anterior third of the cell. Sonderia paramacrochilus sp. nov. closely resembles S. macrochilus but differs mainly by its oral opening being located closer to the anterior cell margin and its spindle-shaped extrusomes. Sonderia steini sp. nov. is a freshwater species that can be recognized by its shallow buccal cavity, sparsely distributed rod-shaped extrusomes, and having 68-79 monokinetidal somatic kineties that form sutures on both sides of the body. Phylogenetic analyses based on small subunit ribosomal RNA (SSU rRNA) gene sequence data support the monophyly of the family Sonderiidae, however, Sonderia is paraphyletic. The genus Sonderia is briefly revised and a key to the identification of species belonging to this genus is supplied.

Effects of nitrofurazone on ecosystem function in marine environments: A case study on microbial fauna

To evaluate the effects of nitrofurazone on functional processes in marine ecosystems, periphytic protozoan communities were exposed to different concentrations of the antibiotic for a 10-day duration. Species trait distributions in the tested communities were observed during exposure to five concentrations of nitrofurazone. A fuzzy coding system with seven traits and seventeen categories was used to summarize the changes in functional patterns of the test organisms. Nitrofurazone had a significant influence on the function process of the periphytic ciliate communities. Bacterivores with flattened bodies were sensitive to the toxicant whereas sessile and cylindrical raptors showed a high tolerance to nitrofurazone, invariably dominating communities exposed to high concentrations. Bootstrapped-average analysis demonstrated a significant change in functional patterns at highest nitrofurazone concentrations (8 mg l^-1). Based on these findings, it is suggested that nitrofurazone may negatively influence ecosystem function in marine environments.

Biodiversity of freshwater ciliates (Protista, Ciliophora) in the Lake Weishan Wetland, China: the state of the art

Ciliates are core components of the structure of and function of aquatic microbial food webs. They play an essential role in the energy flow and material circulation within aquatic ecosystems. However, studies on the taxonomy and biodiversity of freshwater ciliates, especially those in wetlands in China are limited. To address this issue, a project to investigate the freshwater ciliates of the Lake Weishan Wetland, Shandong Province, commenced in 2019. Here, we summarize our findings to date on the diversity of ciliates. A total of 187 ciliate species have been found, 94 of which are identified to species-level, 87 to genus-level, and six to family-level. These species show a high morphological diversity and represent five classes, i.e., Heterotrichea, Litostomatea, Prostomatea, Oligohymenophorea, and Spirotrichea. The largest number of species documented are oligohymenophoreans. A comprehensive database of these ciliates, including morphological data, gene sequences, microscope slide specimens and a DNA bank, has been established. In the present study, we provide an annotated checklist of retrieved ciliates as well as information on the sequences of published species. Most of these species are recorded in China for the first time and more than 20% are tentatively identified as new to science. Additionally, an investigation of environmental DNA revealed that the ciliate species diversity in Lake Weishan Wetland is higher than previously supposed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-022-00154-x.

The taxonomy and molecular phylogeny of two epibiotic colonial peritrich ciliates (Ciliophora, Peritrichia)

Two colonial sessilid peritrichs, Epistylis qingdaoensis n. sp. and Carchesium cyclopidarum Nenninger, 1948, were isolated from a marine crustacean and a freshwater mayfly, respectively. Morphological characters for each species were revealed by in vivo observations and silver staining methods. Epistylis qingdaoensis n. sp. is characterized by the apperance of the colony which is up to 250 μm high and usually contains fewer than eight zooids, the single-layered peristomial lip, the conspicuously conical peristomial disc, and the structure of infundibular polykinety 3 which comprises three isometric ciliary rows. Carchesium cyclopidarum is recognized by the colony height of about 600 μm, the small zooid size of 35-50 × 20-30 μm, and the low number of silverlines. Phylogenetic analyses based on small subunit ribosomal DNA sequences were performed to reveal their evolutionary relationships. Surprisingly, neither species clustered with its congeners. Epistylis qingdaoensis n. sp. nested within a clade of Zoothamnium species that was sister to a clade comprising core Epistylis species and several Zoothamnium species. Carchesium cyclopidarum nested within a clade comprising solitary peritrichs and was distantly related to the type species of Carchesium, C. polypinum. These findings imply for the first time that Carchesium is non-monophyletic.

Insights into the phylogeny of the family Deviatidae (Protozoa, Ciliophora, Hypotrichia) based on multi-gene, morphological and ontogenetic information, with the establishment of a new species Deviata multilineae n. sp

Hitherto, the phylogeny of ciliated protists, an important group of model organisms in many fields, has been mainly based on a single marker gene (SSU rDNA, nuclear small subunit ribosomal RNA gene). However, there is increasing evidence showing this is insufficient to provide robust phylogenies and has resulted in confusing systematics in many ciliates groups. Among these, the phylogenies within family Deviatidae (Spirotrichea, Hypotrichia) are ambiguous due to the dependence on SSU rDNA and undersampling. Here, we provide eight new sequences and conduct phylogenetic analyses based on both multi-gene and single-gene to clarify evolutionary relationships among all deviatids for which gene sequence are available. The results reveal that: (1) the monophyly of Deviatidae is well-supported by both single-gene and concatenated data; (2) the presence of fine cirri and relatively wide spacing of these cirri within all rows are plesiomorphies of Deviatidae; (3) Pseudosincirra longicirrata is closely related to Deviata rositae, which is supported by their shared possession of dorsomarginal kineties; (4) phylogenetic analyses and approximately unbiased test based on multi-gene support a close relationship among taxa lacking dorsomarginal kineties (D. parabacilliformis, D. multilineae nov. spec., D. abbrevescens, D. brasiliensis and Perisincirra paucicirrata); (5) Deviatidae shows a close relationship with Dorsomarginalia and Strongylidium-Hemiamphisiella-Pseudouroleptus assemblage, suggesting the presence/absence of dorsomarginal kineties is phylogenetically informative in this family and presence of them may be a plesiomorphy. Based on the morphological, morphogenetic and phylogenetic data, the evolutionary relationships within Deviatidae are hypothesized, and a new ciliate, Deviata multilineae nov. spec., collected from China, is investigated.

Use of functional units of periphytic protozoa for monitoring water quality in marine ecosystems: bioindicator redundancy

Although periphytic protozoan communities have long been used for the bioassessment of water quality, their utility is hampered by functional redundancy, leading to high "signal-to-noise" ratios. In this study, a 1-year baseline survey of periphytic protozoan communities was carried out in coastal waters of the Yellow Sea, northern China, in order to determine redundancy levels in conditions of differing water quality. Samples were collected at four sampling sites along a pollution gradient. Environmental variables such as salinity, chemical oxygen demand (COD), and concentrations of dissolved oxygen (DO), soluble reactive phosphates (SRP), ammonium nitrogen (NH₄-N), and nitrate nitrogen (NO₃-N) were measured to compare with biotic factors. A total of 53 functional units (FUs) were identified from 144 observed protozoan species based on four biological traits, i.e., feeding type, body size, movement type, and source of food supply. For reducing the "signal-to-noise" ratios of species-abundance/biomass data, the peeling procedure was used to identify the bioindicator redundancy levels based on these FUs. Three consecutive subsets of response units (RU1-RU3) with correlation coefficients > 0.75 of the full FU dataset were identified, comprising 12 FUs, 21 FUs, and 9 FUs, respectively. Algivores and bacterivores were dominant in RU1 and RU2 among the polluted sites, whereas raptors were dominant in RU3 at the unpolluted site. In terms of relative abundance, RU1 was the primary contributor to the protozoan communities during the 1-year cycle and its relative abundance increased with the increasing pollution, whereas RU2 and RU3, with complementary temporal distributions, generally decreased with increasing pollution. Ordinations based on bootstrapped average analyses revealed a significant variation in the functional pattern of all three RUs among the four sampling sites. Biological-environmental match analysis demonstrated that the variability was driven by the increasing concentrations of nutrients (e.g., NH₄-N, NO₃-N, and PO₄-P) and decreasing concentrations of DO (P < 0.05). There were high levels of functional redundancy among periphytic protozoan communities which could be used as bioindicators of marine water quality.

A Case Study of the Morphological and Molecular Variation within a Ciliate Genus: Taxonomic Descriptions of Three Dysteria Species (Ciliophora, Cyrtophoria), with the Establishment of a New Species

Three Dysteria species, D. crassipes Claparède & Lachmann, 1859; D. brasiliensis Faria et al., 1922; and D. paracrassipes n. sp., were collected from subtropical coastal waters of the East China Sea, near Ningbo, China. The three species were studied based on their living morphology, infraciliature, and molecular data. The new species D. paracrassipes n. sp. is very similar to D. crassipes in most morphological features except the preoral kinety, which is double-rowed in the new species (vs. single-rowed in D. crassipes). The difference in the small ribosomal subunit sequences (SSU rDNA) between these two species is 56 bases, supporting the establishment of the new species. The Ningbo population of D. crassipes is highly similar in morphology to other known populations. Nevertheless, the SSU rDNA sequences of these populations are very different, indicating high genetic diversity and potentially cryptic species. Dysteria brasiliensis is cosmopolitan with many described populations worldwide and four deposited SSU rDNA sequences. The present work supplies morphological and molecular information from five subtropical populations of D. brasiliensis that bear identical molecular sequences but show significant morphological differences. The findings of this study provide an opportunity to improve understanding of the morphological and genetic diversity of ciliates.

A community-based approach to analyzing the ecotoxicity of nitrofurazone using periphytic protozoa

The ecotoxicity of nitrofurazone was analyzed based on a community-based approach using periphytic protozoa. Median lethal concentrations (LC₅₀) within an exposure time of 30 min were determined by an acute toxicity test at 0, 1.5, 3, 6 and 12 mg ml^-1 nitrofurazone. Toxicity curve tests demonstrated a decreasing trend with increasing exposure time and was well fitted to the toxicity equation LC₅₀ = 32.85e^-0.8143t (t = exposure time; R² = 0.91; P < 0.05). Median inhibition concentrations (IC₅₀) for periphytic protozoan growth rates were obtained by chronic tests at 0, 1, 2, 4 and 8 mg ml^-1 nitrofurazone within 10 days exposure and were well fitted to the equation r_% = 0.3686e^-0.35Cnit (C_nit is the concentration of nitrofurazone; R² = 0.92 and P < 0.05). These findings suggest that the LC₅₀ and IC₅₀ values of nitrofurazone can be predicted for any exposure time using periphytic protozoan communities as a bioassay model.

Taxonomy and systematics of a new pleurostomatid ciliate, Pseudolitonotus spirelis gen. et sp. n. (Protozoa, Ciliophora, Haptoria)

Recent studies have revealed a high diversity of pleurostomatid ciliates in brackish habitats. Here, a novel species, Pseudolitonotus spirelis gen. et sp. n., isolated from a mangrove wetland of southern China, was investigated based on living observation, protargol staining, and molecular analyses. The new genus Pseudolitonotus gen. n. is characterized by the last left somatic kinety (LKn) being shortened and none of the right somatic kineties extending to the anterior end of the cell, thus distinguishing it from all known pleurostomatid genera. The type species, Pseudolitonotus spirelis sp. n., is characterized by the possession of two macronuclear nodules, 11-15 right and 7-9 left kineties, a single contractile vacuole subterminally located, extrusomes evenly spaced along the entire ventral margin and some forming an "apical group", two types of cortical granules, and the bottom of the oral slit invariably being twisted. Litonotus gracilis (Pan et al. Eur J Protistol 51:494-506, 2015) is believed to be another member of this new genus as its LKn and right somatic kineties are all shortened. Hence, a new combination, Pseudolitonotus gracilis (Pan et al., 2015) comb. n., is suggested and its diagnosis is improved. Molecular phylogenetic analyses based on SSU rDNA sequence data reveal that Pseudolitonotus gen. n. is monophyletic and groups with Apolitonotus (Pan et al. J Eukaryot Microbiol 67:252-262, 2020) of the family Protolitonotidae (Wu et al. Zool Scr 46:245-253, 2017). However, the familial assignment of this new genus is uncertain based on current data.

Insights into the ecotoxicity of nitrofurazone in marine ecosystems based on body-size spectra of periphytic ciliates

In ecotoxicological studies, some biological responses known as biomarkers can be used as powerful tools to evaluate the ecotoxicity. In this study, we investigated the disparity of responses shown by body-size spectra of periphytic ciliate communities when used as biomarkers to detect the toxicity of the broad-spectrum veternary antibiotic nitrofurazone. Briefly, in chronic exposure experiments ciliate communities were exposed to different concentrations (0, 1, 2, 4 and 8 mg ml^-1) of nitrofurazone. Relative Abundance of ciliates in all body-size categories decreased significantly, whereas their frequency of occurrence and probability densities showed hormetic-like responses in a dose dependent manner. Additionally, body-size distinctness indices were influenced by toxic stress and significantly departed from an expectation at higher nitrofurazone concentrations. Taken together, our results demonstrated that body-size spectra and body-size distinctness offered clear evidence of nitrofurazone toxicity in periphytic ciliates. Body-size spectra can therefore be used as a pivotal biomarker to determine the ecotoxicity of nitrofurazone in aquatic environments.

Taxonomic and phylogenetic studies on two new freshwater Amphileptus species (Ciliophora, Pleurostomatida), from Lake Weishan, northern China

The morphology and phylogeny of two new species of pleurostomatid ciliates, Amphilepus weishanensis sp. nov. and A. parapleurosigma sp. nov., collected from Lake Weishan in northern China, were studied using live observation, protargol staining and phylogenetic analyses based on small subunit ribosomal DNA (SSU rDNA) sequence data. In both species, extrusomes form an apical group and contractile vacuoles are distributed along both the dorsal and the ventral margin. Amphileptus weishanensis sp. nov. is characterized by its body size (560-780 × 60-100 μm in vivo) and the possession of five left and 56-61 right somatic kineties, filiform extrusomes and 3-9 macronuclear nodules. Amphileptus parapleurosigma sp. nov. is characterized by possessing 4-6 left and 19-24 right somatic kineties and clavate extrusomes. The SSU rDNA sequences differ among ten similar species by 3-60 bp. Phylogenetic analyses based on the SSU rDNA sequences indicate that the family Amphileptidae is monophyletic while Amphileptus is paraphyletic with Pseudoamphileptus nesting within this genus.

Toxicity of silver nanoparticles (AgNPs) in the model ciliate Paramecium multimicronucleatum: Molecular mechanisms of activation are dose- and particle size-dependent

Current understanding of toxicity mechanisms of nanoparticles is still far from comprehensive, partly because of the neglect of control factors such as the dependence of mechanism activation on the exposure dosage and particle size. To reveal molecular mechanisms of silver nanoparticle (AgNP) toxicity, the model ciliate Paramecium multimicronucleatum was exposed for 12 h to different concentrations of AgNPs with particle size of 20 nm (0.08, 0.12, and 0.30 mg/l) and 40 nm (0.08 and 0.30 mg/l). Transcriptomes of the tested ciliates were then analyzed based on dendrograms of gene expression, Gene Ontology (GO) terms, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, and up- and down-regulated genes. Results showed that: (1) toxicity mechanisms of AgNP revealed by analyses of GO and KEEG were significantly involved in the metabolic pathways of nutrients and the biosynthesis of macromolecules; (2) the top five up-regulated genes were mainly related to biological oxidation, biosynthesis, and oxidative stress, while top five down-regulated genes were mainly related to glycolysis; (3) activated mechanisms varied both in quantity and in type with dosages and particle sizes of AgNPs; (4) AgNP-treatments with different exposure dosages and particle sizes can produce the same toxicity in terms of 12 h-EC₅₀, but the underlying molecular mechanisms differed significantly. In brief, this study provides insights into the molecular mechanisms of AgNP toxicity through transcriptome analyses and confirmed their dependence of activation on the exposure dosage and particle size of AgNPs.

Genetic Diversity and Phylogeny of the Genus Euplotes (Protozoa, Ciliophora) Revealed by the Mitochondrial CO1 and Nuclear Ribosomal Genes

Nuclear ribosomal and mitochondrial genes have been utilized individually or in combination to identify known species and discriminate closely related species. However, compared with metazoans, genetic diversity within the ciliate order Euplotida is poorly known. The aim of this study is to investigate how much nucleotide sequence divergence occurs within Euplotes. A total of 14 new gene sequences, comprising four SSU rDNA and 10 CO1 (including three species for the first time) were obtained. Phylogenetic analyses were carried out based on sequences of two DNA fragments from the same 27 isolates. We found that CO1 revealed a larger interspecific divergence than the SSU rRNA gene, thus demonstrating a higher resolution for separating congeners. Genetic distances differ significantly at the species level. Euplotes balteatus was revealed to have a large intraspecific variation at two loci, while E. vannus showed different levels of haplotype variability, which appeared as a polyphyletic cluster on the CO1 tree. These high genetic divergences suggest the presence of more cryptic species. By contrast, the CO1 gene showed low variability within E. raikovi, appearing as monophyletic clusters, which indicates that this species could be identified based on this gene. Conclusively, CO1 is a suitable marker for the study of genetic diversity within Euplotes, and increased taxon sampling gives an opportunity to screen relationships among members of this genus. Additionally, current data present no clear biogeographical pattern for Euplotes.

Taxonomy and Phylogeny of the Dileptid Ciliate Genus Paradileptus (Protista: Ciliophora), With a Brief Review and Redescriptions of Two Species Isolated From a Wetland in Northern China

Members of the genus Paradileptus are apex predators in microbial food webs. They are often encountered in freshwater biotopes and have been used in research on water quality monitoring and ecology. Nevertheless, our understanding of the biodiversity of Paradileptus, especially its ecological and genetic diversities, is very poor which hinders our ability to understand the ecosystem services it provides. The present study gives a detailed account of two Chinese populations of Paradileptus elephantinus and P. conicus including their living morphology, infraciliature, and molecular phylogenies based on 18S, 5.8S, and ITS ribosomal DNA sequences. The phylogenetic relationships between these two species and other rhynchostomatians are investigated. We also explore the potential contribution of differentiation of the proboscis (e.g., extrusomes, dorsal brush, and differentiated kineties) to niche partitioning and speciation in Paradileptus. The global distribution of Paradileptus is summarized based on published data. Finally, a key to the identification of the valid species of Paradileptus is provided.

Notes on Homalogastra similis nom. nov. (Ciliophora, Scuticociliatia), a replacement name for the junior homonym Homalogastra binucleata Liu et al., 2020

We recently established a new species, Homalogastra binucleata, with a morphological description and phylogenetic analyses based on SSU rRNA gene sequence data (Liu et al., 2020). Helmut Berger (Salzburg, Austria) commented that Homalogastra binucleata Liu et al., 2020 is a junior primary homonym of H. binucleata Song, 1993, the latter having been transferred to the genus Uronemita by Liu et al. (2016). According to article 57.2 of the ICZN (1999), the junior primary homonym, Homalogastra binucleata Liu et al., 2020, is permanently invalid. It is replaced by Homalogastra similis nom. nov.

Redescription and molecular characterization of two Trichodina species (Ciliophora, Peritrichia, Mobilida) from freshwater fish in China

During an investigation of parasitic ciliates in northern China, two Trichodina species, T. acuta Lom, 1970 and T. nigra Lom, 1960, were isolated from the freshwater fish Cyprinus carpio Linnaeus, 1758. The morphology of each species was investigated based on dry silver nitrate-stained specimens. In addition, the molecular phylogeny of each was analyzed based on small subunit ribosomal DNA (SSU rDNA) sequence data. Trichodina acuta can be distinguished from its congeners by the undefined periphery of the central circle, the distinct gap between the rays and the central circle, and the distinctly sickle-shaped blades. Trichodina nigra is a cosmopolitan ciliate and is characterized by its densely linked denticles, broad, rounded spatula-shaped blades, robust central parts, and well developed rays. Phylogenetic analyses revealed that T. acuta and T. nigra nest within different clades, supporting the assertion that the GC content of SSU rDNA sequences could reflect evolutionary relationships among Trichodina species.

Overview of the Diversity, Phylogeny and Biogeography of Strombidiid Oligotrich Ciliates (Protista, Ciliophora), With a Brief Revision and a Key to the Known Genera

Strombidiids are common free-living ciliates that have colonized coastal and open oceanic waters across the world. In recent years, numerous new taxa and gene sequences of strombidiids have been reported, revealing a large diversity of both their morphologic and genetic features. Here, we compare the taxonomic characters of all genera in the family Strombidiidae, provide a key to their identification, and investigate their molecular phylogeny. In addition, we analyze their regional distribution based on faunal data accumulated in China and attempt to infer their global distribution based on SSU rRNA gene sequence data. The current work revises the systematics of strombidiids based on morphologic, phylogenetic, and biogeographic evidence and provides a genus-level review of marine strombidiids.

The Morphology, Taxonomy, and Phylogenetic Analyses of Five Freshwater Colonial Peritrich Ciliates (Alveolata, Ciliophora), Including the Descriptions of Two New Species

The morphology and phylogeny of two new sessilid species, Zoothamnium weishanicum n. sp. and Epicarchesium sinense n. sp., two insufficiently known species, Zoothamnium arbusculaEhrenberg, 1831 and Zoothamnium hentscheliKahl, 1935, and a well-known species, Carchesium polypinum (Linnaeus, 1767) Ehrenberg, 1838, collected from freshwater habitats of China, were investigated. Zoothamnium weishanicum n. sp. is characterized by its inverted bell-shaped zooids, double-layered peristomial lip, alternately branched stalk, and two different-length rows in infundibular polykinety 3 (P3). Epicarchesium sinense n. sp. is recognized by its asymmetric-pyriform zooids, single-layered peristomial lip, conspicuous cortical blisters on the pellicle, dichotomously branched stalk, and P3 containing one short inner row and two long outer rows. Based on previous and newly obtained data of the three known species, improved diagnoses and redescriptions are provided including, for the first time, data on the infraciliature of Z. arbuscula and Z. hentscheli. In addition, we analyzed the phylogeny of each species based on SSU rDNA sequence data.

Taxonomy and SSU rDNA-Based Phylogeny of Two Heterotrich Ciliates (Ciliophora, Heterotrichea) Collected From Subtropical Wetlands of China, Including the Description of a New Species, Linostomella pseudovorticella n. sp

The Heterotrichea Stein, 1859 are a group of ciliated protists (single-celled eukaryotes) that occur in a wide variety of aquatic habitat where they play important roles in the flow of nutrients and energy within the microbial food web. Many species are model organisms for research in cytology and regenerative biology. In the present study, the morphology and phylogeny of two heterotrich ciliates, namely, Linostomella pseudovorticella n. sp. and Peritromus kahli Villeneuve-Brachon, 1940, collected from subtropical wetlands of China, were investigated using morphological and molecular methods. L. pseudovorticella n. sp. differs from its only known congener, Linostomella vorticella Ehrenberg, 1833 Aescht in Foissner et al., 1999, by having more ciliary rows (48-67, mean about 56 vs. 26-51, mean about 42) and its small-subunit (SSU) rDNA sequence, which shows a 15-bp divergence. Although P. kahli has been reported several times in recent decades, its infraciliature has yet to be described. A redescription and improved diagnosis of this species based on a combination of previous and present data are here supplied. Phylogenetic analyses based on SSU rDNA sequences revealed that the genus Linostomella is positioned within Condylostomatidae, and Peritromidae is sister to Climacostomidae with relatively low support, and the family Spirostomidae is the root branch of the class Heterotrichea.

Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea)

The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.