Small subunit ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1 gene sequences of 21 strains of the parasitic scuticociliate Miamiensis avidus (Ciliophora, Scuticociliatia)

Miamiensis avidus, a Novel Scuticociliate Pathogen Isolated and Identified from Cultured Large Yellow Croaker (Larimichthys crocea)

Scuticociliates are recognized as the causative agents of mass mortalities in certain cultured marine fishes, resulting in enormous economic losses. This study aimed to investigate a fatal infection caused by scuticociliates in farmed large yellow croaker (Larimichthys crocea) in Fujian province, China. Microscopic examinations of focal organs, including the brain, eyes, gills, and skin, revealed the presence of parasites. Active masses of scuticociliates were observed in these organs, and the ciliates were subsequently isolated and maintained in vitro. An immersion challenge experiment revealed that L. crocea experienced cumulative mortalities reaching 73% within 7 d upon exposure to 1.0 × 104 ciliates mL-1. Based on the microscopic and PCR testing of infected fishes, the brain was comprehensively inferred as the main infection organ for the isolated strain. Microscopic and submicroscopic observations of the isolated scuticociliate, coupled with cortical ciliature patterns revealed through α-tubulin indirect immunofluorescence techniques, identified these scuticociliates as Miamiensis avidus. The sequencing of two genetic markers (small subunit ribosomal RNA, SSU rRNA and cytochrome c oxidase subunit I, COI) further confirmed that the isolated strains exhibited the highest sequence similarity to most M. avidus sequences in GenBank. However, significant differences in SSU sequences compared to the M. avidus strain Ma/2, and the lack of published COI and ITS (internal transcribed spacer) sequences for Ma/2, indicate the need for further molecular data to resolve whether there are potential cryptic species within the M. avidus complex.

Formulation of chitosan microsphere-based oral vaccine against the scuticociliate parasite Miamiensis avidus: Evaluation of its protective immune potency in olive flounder (Paralichthys olivaceus)

Miamiensis avidus is a parasitic pathogen that causes scuticociliatosis, a severe and often lethal marine infection that affects marine fishes worldwide, including olive flounder (Paralichthys olivaceus) in Korea. This parasite infects all size groups of flounder year-round, causing recurring mortalities and huge economic losses to the Korean flounder industry each year. However, few efforts have been made to implement effective remedial measures to control this parasite. Therefore, our study sought to develop a chitosan microsphere (MS)-encapsulated inactivated vaccine (IMa + chitosan) for oral delivery (adsorbed in feed) to flounder fingerlings and assess its protective efficacy at different modalities via three in vivo experimental trials. Immunisation trial-1 was conducted to determine the effective concentration of chitosan. Our findings indicated that an IMa + chitosan 0.05 % vaccine formulation was safe and effective in providing moderate protection [46.67%-53.3 % relative percent survival (RPS)] against M. avidus intraperitoneal (IP) injection challenge at two weeks post-vaccination (wpv) compared to the IMa + chitosan 0.01 % and IMa + chitosan 0.005 % vaccines (0%-13.3 % RPS) irrespective of the antigen doses. In trial-2, the IMa + chitosan 0.05 % vaccine elicited similar protective immunity (30.8%-57.1 % RPS) in olive flounder against M. avidus at varying antigen doses (high: 2.38 × 106 cells/fish; low: 1.5 × 105 cells/fish), immunisation periods (2 and 5 wpv), and challenge modes (IP injection and immersion). Furthermore, experimental trial-3 validated the use of chitosan MS as an IMa antigen carrier to improve survivability (41.7 % RPS) in the host by significantly (p < 0.05) upregulating specific anti-M. avidus antibody titres in the fish sera and mucus of the group immunised with IMa-containing chitosan MS. In contrast, non-specific immunomodulatory effects (16.7 % RPS and enhanced mucosal antibody titres) were observed in the group treated with chitosan MS without IMa. Therefore, our findings suggested that oral administration of chitosan MS (0.05 %)-encapsulated IMa vaccine is a promising immunisation strategy against M. avidus that can protect the IMa antigen from digestive degradation, facilitates its targeted delivery to the host immune organs, and helps in orchestrating protective immune induction in olive flounder, thus controlling parasite infection.

Characterization of the complete mitochondrial genome of Miamiensis avidus causing flatfish scuticociliatosis

Miamiensis avidus is a parasitic pathogen that causes the disease scuticociliatosis in teleost fish species. It is a ciliate and a free-living marine protozoan belonging to the order Philasterida, subclass Scuticociliatida, class Oligohymenophorea, and phylum Ciliophora. The complete mt-genome of M. avidus was linear and 38,695 bp in length with 47 genes, including 40 protein-coding genes, two ribosomal RNA (rRNA) genes, and five transfer RNA (tRNA) genes. Of these, 20 genes typically belong to the clusters of orthologous groups, playing roles in energy production and conversion, translation, ribosomal structure and biogenesis, and defense mechanisms. This is the first report of sequencing and characterization of the mt-genome of M. avidus, which was observed to be linear and possessing the typical ciliate mitochondrial genome organization and phylogenetic relationships. Remarkable differences were observed between M. avidus and other ciliates in the mitochondrially encoded rRNAs, extensive gene loss in ribosomal genes and tRNAs, terminal repeat sequences, and stop codon usage. A comparative and phylogenetic analysis of M. avidus and Uronema marinum of the order Hymenostomatida, which is most closely related to the order Philasterida, signified the promise of the mitogenome data of M. avidus as a valuable genetic marker in species detection and taxonomic research. The present study has potential applications in epidemiological studies and host-parasite interaction investigations facilitating disease control.

Antiparasitic potential of ethanolic extracts of Carpesii Fructus against Miamiensis avidus in hirame natural embryo cell line and their effects on immune response- and biotransformation-related genes

Scuticociliatosis, caused by Miamiensis avidus, is a severe parasitic disease affecting marine organisms, particularly Paralichthys olivaceus. The aim of this study was to assess the antiparasitic potential of ethanolic extracts of Carpesii Fructus (EECF), the dried fruit of Carpesium abrotanoides L., which is used in traditional Chinese medicine, in vitro. We found that 50%, 70%, and 100% EECF induced morphological changes in M. avidus, including reduced motility, cell shrinkage, and lysis. Nearly 100% cell lysis was observed in M. avidus after 2 h of treating with 100% EECF. After 24 h, the survival rates of M. avidus treated with 100%, 70%, and 50% EECF were 10%, 20%, and 30%, respectively. Additionally, the mRNA levels of immune response-related (IL-1β, IL-8, TNF-α, and CD8-α) and biotransformation-related (CYP1A, CYP1B, CYP3A4, and UGT2B19) genes increased with 70% and 100% EECF treatment and decreased with 50% EECF treatment following pretreatment with concanavalin A. The viability of hirame natural embryo (HINAE) cells was reduced by 50%, 70%, and 100% EECF (100 mg/L) and was between 67 and 80%. The IC₅₀ values of 50%, 70%, 90%, and 100% EECF in HINAE cells were 102.3, 42.93, 39.15, and 38.39 mg/L, respectively. These results indicated that 50% EECF was less toxic to HINAE cells than 70% or 100% EECF, while still exhibiting antiparasitic activity against M. avidus. Therefore, we demonstrated the role of EECF as a natural antiparasitic agent against M. avidus. Our findings suggest that Carpesii Fructus has potential use as an antiparasitic agent in the aquaculture industry.

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.

Comparison of mitochondrial genome and development of specific PCR primers for identifying two scuticociliates, Pseudocohnilembus persalinus and Uronema marinum

Background

Pseudocohnilembus persalinus and Uronema marinum (Ciliophora, Scuticociliatia), as parasitic scuticociliatid ciliates, were isolated from Scophthalmus maximus and Takifugu rubripes, respectively, in our previous studies. These ciliates are morphologically very similar; hence, it is difficult to identify specific scuticociliate species using traditional classification methods for performing taxonomic research and disease control studies.

Methods

We annotated the mitochondrial genomes of these two scuticociliates on the basis of previous sequencing, including analyses of nucleotide composition, codon usage, Ka/Ks, and p-distance. We also compared the nucleotide and amino acid similarity of the mitochondrial genomes of P. persalinus, U. marinum, and other 12 related ciliates, and a phylogenetic tree was constructed using 16 common genes. We chose the nad4 and nad7 genes to design specific PCR primers for identification.

Results

P. persalinus and U. marinum were found to have a close evolutionary relationship. Although codon preferences were similar, differences were observed in the usage of codons such as CGA, CGC, and GTC. Both Ka/Ks and p-distance were less than 1. Except for yejR, ymf57, ymf67, and ymf75, the amino acid sequence similarity between P. persalinus and U. marinum was greater than 50%.

Conclusions

The mitochondrial genomes of P. persalinus and U. marinum were thoroughly compared to provide a reference for disease prevention and control. The specific PCR primers enabled us to identify P. persalinus and U. marinum rapidly and accurately at the molecular level, thus providing a basis for classification and identification.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04821-3.

Molecular identification of Uronema marinum (Protozoa, Ciliophora, Scuticociliatia) in cultured turbot (Psetta maxima) larvae

Scuticociliates are dangerous parasitic pathogens causing systemic tissue destruction and high mortality in marine fish worldwide. In this study, the first identification of Uronema marinum (Ciliophora, Scuticociliatida) from cultured turbot (Psetta maxima) larvae using mitochondrial cytochrome c oxidase 1 (cox1) gene sequence as well as species-specific primers was reported. The mean prevalence values of infected fish were calculated, and partial sequencing obtained from the mitochondrial cox1 gene region was also compared with isolates registered in the Genbank database. The sequence comparison showed 93.00% identity to U. marinum, and the parasite has also been deposited in the GenBank database. This study is the first case of U. marinum infection in Turkish marine aquaculture, contributing to the systematics and molecular epidemiology of scuticociliate in Turkey.

Some morphologically distinguishable hypotrich ciliates share identical 18S rRNA gene sequences – taxonomic insights from a case study on Oxytricha species (Protista, Ciliophora)

Modern taxonomic studies of ciliated protozoa require both morphological and molecular data. One dilemma is how to distinguish morphologically similar species with few nucleotide differences in the widely used marker, the 18S rRNA gene. In the present study, two Oxytricha species were morphologically documented using light and electron microscopy. The mitochondrial cytochrome c oxidase subunit I (COI) gene and a fragment of the rRNA gene covering the 18S-ITS1-5.8S-ITS2-28S rRNA gene regions were sequenced. Phylogenetic analyses of all available Oxytricha granulifera-related populations were performed to reveal the internal relationships of this group. We described a new species, Oxytricha atypica sp. nov., distinguished from its congeners by having seven postoral ventral cirri resulting from the additional fragmentation of anlage V during ontogenesis. Although their 18S rRNA genes differ by only one nucleotide, divergence of the COI gene is as high as 11.8% between O. atypica and the closely related species, O. granulifera. All but one of the COI nucleotide substitutions were synonymous. We documented the highly conserved nature of the 18S rRNA gene in the morphospecies of Oxytricha. Based on these findings, we speculate that O. granulifera contains cryptic species or morphospecies needing further characterization, and new insights for the taxonomy of hypotrich ciliates are also discussed.

METAGENOMIC NEXT-GENERATION SEQUENCING REVEALS MIAMIENSIS AVIDUS (CILIOPHORA: SCUTICOCILIATIDA) IN THE 2017 EPIZOOTIC OF LEOPARD SHARKS ( TRIAKIS SEMIFASCIATA) IN SAN FRANCISCO BAY, CALIFORNIA, USA

During March to August of 2017, hundreds of leopard sharks ( Triakis semifasciata) stranded and died on the shores of San Francisco Bay, California, US. Similar mass stranding events occurred in 1967 and 2011, but analysis of those epizootics was incomplete, and no etiology was confirmed. Our investigation of the 2017 epizootic revealed severe meningoencephalitis in stranded sharks, raising suspicion for infection. We pursued a strategy for unbiased pathogen detection using metagenomic next-generation sequencing followed by orthogonal validation and further screening. We showed that the ciliated protozoan pathogen, Miamiensis avidus, was present in the central nervous system of leopard ( n=12) and other shark species ( n=2) that stranded in San Francisco Bay but was absent in leopard sharks caught elsewhere. This ciliated protozoan has been implicated in devastating outbreaks in teleost marine fish but not in wild elasmobranchs. Our results highlight the benefits of adopting unbiased metagenomic sequencing in the study of wildlife health and disease.

Utility of mitochondrial CO1 sequences for species discrimination of Spirotrichea ciliates (Protozoa, Ciliophora)

Ciliates are a diverse species group of the Protozoa, and nuclear and mitochondrial genes have been utilized to discover new species and discriminate closely related species. The mitochondrial cytochrome c oxidase subunit 1 (CO1) gene has been used to discriminate metazoan species and has also been applied for some groups in the phylum Ciliophora. However, it is difficult to produce a universal primer as a standard barcode, because unlike metazoans, mitochondrial DNA sequences of ciliates are long and highly variable. Therefore, to design the new primer set, we sequenced the mitochondrial genomes of two pseudokeronopsids in the class Spirotrichea using next-generation sequencing technology (HiSeq™ 2000). Based on putative CO1 gene fragments of the pseudokeronopsids, we designed the new primer set and successfully sequenced the CO1 of 69 populations representing 47 species (five orders, 14 families, and 27 genera). We found that CO1 showed higher resolution for separating congeneric species than did nuclear SSU rRNA gene sequences, and we identified some putative cryptic species.

New data on flatfish scuticociliatosis reveal that Miamiensis avidus and Philasterides dicentrarchi are different species

Scuticociliatosis is a severe disease in farmed flatfish. However, the causative agent is not always accurately identified. In this study, we identified two isolates of scuticociliates from an outbreak in cultured fine flounder Paralichthys adspersus. Scuticociliate identification was based on morphological data, examination of life stages and the use of molecular approaches. The isolates were compared with a strain of Philasterides dicentrachi from turbot Scophthalmus maximus and with a strain deposited in the American Type Culture Collection as Miamiensis avidus ATCC® 50180™. The use of morphological, biological and molecular methods enabled us to identify the isolates from the fine flouder as P. dicentrarchi. Comparison of P. dicentrachi isolates and M. avidus revealed some differences in the buccal apparatus. Unlike P. dicentrarchi, M. avidus has a life cycle with three forms: macrostomes (capable of feeding on P. dicentrarchi), microstomes and tomites. Additionally, we found differences in the 18S rRNA and α- and β-tubulin gene sequences, indicating that P. dicentrarchi and M. avidus are different species. We therefore reject the synonymy/conspecificity of the two taxa previously suggested. Finally, we suggest that a combination of morphological, biological, molecular (by multigene analysis) and serological techniques could improve the identification of scuticociliates parasites in fish.

First isolation of Miamiensis avidus (Ciliophora: Scuticociliatida) associated with skin ulcers from reared pharaoh cuttlefish Sepia pharaonis

In the winter of 2015, a skin ulcer disease outbreak occurred in a pharaoh cuttlefish Sepia pharaonis population cultured on a land-based fish farm in China. Affected cuttlefish (about 60% of the population) were characterized as having developed ulcers on the dorsal skin, fin fringe, or distal mantle tip. Masses of a ciliated protozoan were isolated from skin ulcers. The ciliate was identified as Miamiensis avidus based on the morphological features of living and protargol-impregnated specimens. This identification was also supported by high sequence similarity of the small subunit ribosomal RNA gene (100%) and another ribosomal DNA region (including the 2 internal transcribed spacers and the 5.8S gene; 99%) with published sequences of fish parasitic M. avidus strains. M. avidus is known to be a histophagous marine fish parasite. This report describes the first case of M. avidus associated with skin ulcers in a cephalopod mollusk (Mollusca, Cephalopoda). This finding suggests that M. avidus may infect a phylogenetically broader range of hosts than what has previously been reported. Furthermore, M. avidus may pose a health risk to hatchery-reared cephalopods.

Identification of the pathogenic ciliate Pseudocohnilembus persalinus (Oligohymenophorea: Scuticociliatia) by fluorescence in situ hybridization

Many scuticociliatid ciliates are regarded as devastating pathogens in aquaculture. Among these, Pseudocohnilembus persalinus is a facultative pathogen that often results in refractory diseases of mariculture fish. Although traditional silver staining methods have been successfully used to identify these ciliates, their identification is hampered by their small size and their morphological similarity to closely related species. We designed an alternative method of identification of P. persalinus using an SSU-rDNA targeted oligonucleotide probe labeled with a fluorochrome, and optimized in a fluorescence in situ hybridization (FISH) protocol. The assay results in a clear identification by strong fluorescence signals from the oligonucleotide probe. The method can be used for quick and early detection of P. persalinus infections on host fish, as well as other susceptible organisms in aquiculture water. It may also be used in studies of the geographical distribution of this scuticociliate.