Ultrastructural study on a novel microsporidian, Endoreticulatus eriocheir sp. nov. (Microsporidia, Encephalitozoonidae), parasite of Chinese mitten crab, Eriocheir sinensis (Crustacea, Decapoda)

Multi-omics analysis of oxidative stress and apoptosis in hepatopancreas cells induced by Polyascus gregaria parasitizing the Eriocheir sinensis

Polyascus gregaria, a parasitic barnacle, poses a significant threat to Eriocheir sinensis farms by inhibiting crab growth. However, the molecular and pathological mechanisms behind P. gregaria infection in the hepatopancreas of E. sinensis remain unclear. In this study, we investigated the impact and underlying mechanisms of P. gregaria infection on E. sinensis through analyzing the infected hepatopancreatic tissues by tandem mass tag technology and RNA-Seq high-throughput sequencing. Among the identified 10,693 differentially expressed genes, 294 genes were significantly altered following P. gregaria infection, including 92 upregulated and 202 downregulated genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses further revealed the involvement of these genes in oxidative decomposition, lipid metabolism, inflammation, and hepatopancreas metabolism. Meanwhile, the identified 253 differentially expressed proteins, including 143 upregulated and 110 downregulated proteins, are mainly related to cellular and metabolic processes, catalytic activity, and cell components. The pathway analysis indicated their enrichment in glycolysis/gluconeogenesis, oxidative phosphorylation, endoplasmic reticulum protein processing, and actin cytoskeleton regulation. The involvement of these differentially expressed genes and proteins in the peroxisome proliferator-activated receptors pathway during host immune responses against P. gregaria infection has been highlighted. Furthermore, pathological examinations and biochemical indicators jointly demonstrated the hepatopancreatic damage and increased oxidative stress and apoptosis in the infected E. sinensis. Collectively, our study provides crucial insights into the mechanisms underlying the E. sinensis-P. gregaria interactions, and may contribute to the development of novel strategies for parasite control and reducing economic losses in aquaculture.

Pseudohepatospora borealis n. gen. n. sp. (Microsporidia: Enterocytozoonida): A microsporidian pathogen of the Jonah crab (Cancer borealis)

The microsporidian diversity catalogued so far has resulted in the development of several taxonomic groups, one of which is the Enterocytozoonida - a group of generalist 'ultimate opportunists', which infect many fished and aquacultured animals, as well as a broad suite of host taxa, including humans. In this study, we provide phylogenetic, ultrastructural, developmental, and pathological evidence for the creation of a new genus and species to hold a microsporidian parasite of the Jonah crab, Cancer borealis. Cancer borealis represents a species of commercial interest and has become the target of a recently developed fishery on the USA and Canadian Atlantic coast. This species was found to harbour a microsporidian parasite that develops in the cytoplasm of alpha and beta cells of the hepatopancreas. We retrieved a 937 bp fragment of the parasite SSU region, alongside developmental and ultrastructural data that suggests this species is ∼ 87 % similar to Parahepatospora carcini and develops in a similar manner in direct association with the host cell cytoplasm. The mature spores are ovoid in shape and measure 1.48 ± 0.15 µm (SD) in length and 1.00 ± 0.11 µm (SD) in width. Phylogenetically, the new parasite clades in the Enterocytozoonida on the same branch as P. carcini. We provide a new genus and species to hold the parasite: Pseudohepatospora borealis n. gen. n. sp. (Microsporidia: Enterocytozoonida) and explore the likelihood that this species may fit into the Hepatoporidae family.

Using average nucleotide identity (ANI) to evaluate microsporidia species boundaries based on their genetic relatedness

Microsporidia are obligatory intracellular parasites related to fungi and since their discovery their classification and origin has been controversial due to their unique morphology. Early taxonomic studies of microsporidia were based on ultrastructural spore features, characteristics of their life cycle and transmission modes. However, taxonomy and phylogeny based solely on these characteristics can be misleading. SSU rRNA is a traditional marker used in taxonomical classifications, but the power of SSU rRNA to resolve phylogenetic relationships between microsporidia is considered weak at the species level, as it may not show enough variation to distinguish closely related species. Overall genome relatedness indices (OGRI), such as average nucleotide identity (ANI), allows fast and easy-to-implement comparative measurements between genomes to assess species boundaries in prokaryotes, with a 95% cutoff value for grouping genomes of the same species. Due to the increasing availability of complete genomes, metrics of genome relatedness have been applied for eukaryotic microbes taxonomy such as microsporidia. However, the distribution of ANI values and cutoff values for species delimitation have not yet been fully tested in microsporidia. In this study we examined the distribution of ANI values for 65 publicly available microsporidian genomes and tested whether the 95% cutoff value is a good estimation for circumscribing species based on their genetic relatedness.

Effects of Dietary L-TRP on Immunity, Antioxidant Capacity and Intestinal Microbiota of the Chinese Mitten Crab (Eriocheir Sinensis) in Pond Culture

L-tryptophan (L-TRP) is an essential amino acid for the normal growth of crustaceans. As a nutritional supplement and antioxidant, L-TRP has the function of immune and antioxidant capacity regulation. From July to November, the effects of L-TRP on the immunity, antioxidant capacity and intestinal microflora of the Chinese mitten crab (Eriocheir sinensis) in pond culture were investigated. After feeding an L-TRP diet for 30 (named as August), 60 (named as September) and 106 (named as November) days, respectively, the activities of the immune and antioxidant enzymes in the hepatopancreas and hemolymph were evaluated, and the intestinal microbiota were profiled via high-throughput Illumina sequencing. The results showed that supplementation of L-TRP significantly increased the activities of AKP in the hepatopancreas in September, and significantly increased the activities of ACP in the hepatopancreas in August and September, and the hemolymph’s ACP activities also significantly increased in August and November (p < 0.05). Similarly, the activities of SOD, AOC and POD in the hepatopancreas significantly increased in September and November (p < 0.05) after feeding the L-TRP diet; meanwhile, the activities of SOD and AOC in the hemolymph also significantly increased in August (p < 0.05). However, in August, the L-TRP diet resulted in a significant increase in MDA activity in the hepatopancreas and hemolymph (p < 0.05). In addition, the results of the intestinal microbiota analysis showed that Firmicutes, Bacteroidetes and Proteobacteria were the dominant phyla in August, September and November, and Patescibacteria was the dominant phylum in September and November. After feeding the L-TRP diet, the richness of Cyanobacteria and Desulfobacterota significantly increased in August (p < 0.05), and the richness of Actinobacteriota significantly decreased in September (p < 0.05). Moreover, the L-TRP supplementation significantly reduced the abundance of ZOR0006 in the Firmicutes in September (p < 0.05). In conclusion, dietary L-TRP could improve the immunity and antioxidant ability and impact the intestinal health of E. sinensis at the early stage of pond culturing. However, long-term feeding of an L-TRP diet might have no positive impact on the activities of the immune, antioxidant enzymes and intestinal microbiota.

Full-length transcriptome sequencing and comparative transcriptome analysis of Eriocheir sinensis in response to infection by the microsporidian Hepatospora eriocheir

As a new generation of high-throughput sequencing technology, PacBio Iso-Seq technology (Iso-Seq) provides a better alternative sequencing method for the acquisition of full-length unigenes. In this study, a total of 22.27 gigabyte (Gb) subread bases and 128,614 non-redundant unigenes (mean length: 2,324 bp) were obtained from six main tissues of Eriocheir sinensis including the heart, nerve, intestine, muscle, gills and hepatopancreas. In addition, 74,732 unigenes were mapped to at least one of the following databases: Non-Redundant Protein Sequence Database (NR), Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), KEGG Orthology (KO) and Protein family (Pfam). In addition, 6696 transcription factors (TFs), 28,458 long non-coding RNAs (lncRNAs) and 94,230 mRNA-miRNA pairs were identified. Hepatospora eriocheir is the primary pathogen of E. sinensis and can cause hepatopancreatic necrosis disease (HPND); the intestine is the main target tissue. Here, we attempted to identify the key genes related to H. eriocheir infection in the intestines of E. sinensis. By combining Iso-Seq and Illumina RNA-seq analysis, we identified a total of 12,708 differentially expressed unigenes (DEUs; 6,696 upregulated and 6,012 downregulated) in the crab intestine following infection with H. eriocheir. Based on the biological analysis of these DEUs, several key processes were identified, including energy metabolism-related pathways, cell apoptosis and innate immune-related pathways. Twelve selected genes from these DEUs were subsequently verified by quantitative real-time PCR (qRT-PCR) analysis. Our findings enhance our understanding of the E. sinensis transcriptome and the specific association between E. sinensis and H. eriocheir infection.

The Innate Immune Response to Infection by Polyascus gregaria in the Male Chinese Mitten Crab (Eriocheir sinensis), Revealed by Proteomic Analysis

The Chinese mitten crab (Eriocheir sinensis) is a representative catadromous invertebrate of the Yangtze River and a commercial species widely cultivated in China. Both cultivated and wild crabs suffer from a variety of parasites and pathogens, which can result in catastrophic economic losses in aquaculture revenue. Polyascus gregaria, a parasitic barnacle with a highly derived morphology, is specialized in invading these crabs. This study examines the immunological mechanism in E. sinensis infected with P. gregaria. Tandem mass tags (TMT), a specialized method of mass-spectrometry, was used to analyze the infection by P. gregaria resistance at the protein level. In the hepatopancreas of infected crabs, 598 proteins differentially expressed relating to physiological change, of which, 352 were upregulated and 246 were downregulated. Based on this differential protein expression, 104 GO terms and 13 KEGG pathways were significantly enriched. Differentially expressed proteins, such as ATG, cathepsin, serpin, iron-related protein, Rab family, integrin, and lectin, are associated with the lysosome GO term and the autophagy-animal KEGG pathways, both of which likely relate to the immune response to the parasitic P. gregaria infection. These results show the benefit of taking a detailed, protein-level approach to understanding the innate immune response of aquatic invertebrates to macroparasite infection.

Morphological and molecular characterization of a new species, Agglomerata daphniae n. sp. from the hypoderm of Daphnia magna (Crustacea: Daphniidae)

A new microsporidian species was described from the hypoderm of Daphnia magna sampled from gibel carp (Carassius auratus gibelio) ponds located in Wuhan city, China. The infected cladocerans generally appeared opaque due to numerous plasmodia distributed in the host integument. The earliest stages observed were uninucleate meronts that were in direct contact with the host cell cytoplasm. Meronts developed into multinucleate sporogonial plasmodia enclosed in sporophorous vesicles. Sporoblasts were produced by the rosette-like division of sporogonial division. Mature spores were pyriform and monokaryotic, measuring 4.48 ± 0.09 (4.34-4.65) µm long and 2.40 ± 0.08 (2.18-2.54) µm wide. The polaroplast was bipartite with loose anterior lamellae and tight posterior lamellae. Polar filaments, arranged in two rows, were anisofilar with two wider anterior coils, and five narrower posterior coils. The exospore was covered with fibrous secretions and was composed of four layers. Phylogenetic analysis based on the obtained SSU rDNA sequence, indicated that the present species clustered with three unidentified Daphnia pulicaria-infecting microsporidia with high support values to form a monophyletic lineage, rather than with the congener, Agglomerata cladocera. The barcode motif of the internal transcribed spacer (ITS) region of the novel species was unique among representatives of the "Agglomeratidae" sensu clade (Vávra et al., 2018). Based on the morphological characters and SSU rDNA-inferred phylogenetic analyses, a new species was erected and named as Agglomerata daphniae n. sp. This is the first report of zooplankton-infecting microsporidia in China.

Transcriptome analysis of hepatopancreas of Eriocheir sinensis with hepatopancreatic necrosis disease (HPND)

Hepatopancreatic necrosis disease (HPND) is a newly emerging disease in the Chinese mitten crab, Eriocheir sinensis, which has resulted in large economic losses. However, the underlying cause of this disease remains unclear. To better understand the pathogenesis and pathogenic mechanism of HPND, we compared the transcriptome differences of the hepatopancreas of E. sinensis with and without HPND. The analysis yielded > 30 million reads for each sample of three test (with HPND) and three control groups (without HPND). We observed 978 downregulated genes and 644 upregulated genes. Among the gene ontology categories "biological process," "cellular component," and "molecular function", the subcategories cellular process, single-organism process, biological regulation, metabolic process, cell part, organelle, organelle part, binding, and catalytic were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that "metabolism of xenobiotics by cytochrome P450," "drug metabolism-cytochrome P450," "chemical carcinogenesis," and "material metabolism" were the "five" most significantly enriched pathways in the hepatopancreas of E. sinensis with HPND. The results revealed that material metabolic abnormalities and drug effects from the external environment might be associated with HPND in the Chinese mitten crab. Considering the wide use of pyrethroids for pond cleaning in Xinghua city, we speculated that pyrethroids might cause HPND in the Chinese mitten crab. Our study provided useful information about the cause and pathogenetic mechanisms of HPND and could help to prevent this disease in production practice.

An integrated metabolic consequence of Hepatospora eriocheir infection in the Chinese mitten crab Eriocheir sinensis

Despite the economic and evolutionary importance of aquatic host-infecting microsporidian species, at present, limited information has been provided about the microsporidia-host interactions. This study focused on Hepatospora eriocheir, an emerging microsporidian pathogen for the Chinese mitten crab Eriocheir sinensis. Hypertrophy of hepatopancreas cells was a common feature of H. eriocheir infection. More importantly, mitochondria of the hepatopancreas were drawn around the H. eriocheir, most likely to aid the uptake of ATP directly from the host. To better understand the crab anti-microsporidian response, de novo transcriptome sequencing of the hepatopancreas tissue was furtherly proceeded. A total of 47.84 M and 57.21 M clean reads were generated from the hepatopancreas of H. eriocheir infected and control groups respectively. Based on homology searches, functional annotation with 6 databases (Nr, Swiss-Prot, KEGG, KOGs, Pfam and GO) for 88,168 unigenes was performed. 2619 genes were identified as differently up-regulated and 2541 genes as differently down-regulated. Prominent functional categories enriched with differentially expressed genes (DEGs) were "ATP binding", "mitochondrion and extracellular region", "oxygen transporter activity", "oxidoreductase activity", "alanine, aspartate and glutamate metabolism", "carbohydrate metabolic process", "starch and sucrose metabolism" and "fatty acid biosynthesis". These results confirmed a parasite external energy supply and an integrated metabolic stress. In addition, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were also identified from the gene library. Taken together, these findings allow us to better understand the underlying mechanisms regulating interactions between H. eriocheir and the crab E. sinensis.

Development of In situ hybridization and real-time PCR assays for the detection of Hepatospora eriocheir, a microsporidian pathogen in the Chinese mitten crab Eriocheir sinensis

A microsporidian parasite, Hepatospora eriocheir, is an emerging pathogen for the Chinese mitten crab Eriocheir sinensis. Currently, there is scant information about the way it transmits infection in the crustacean of commercial importance, including its pathogenesis, propagation and infection route in vivo. In this study, chromogenic in situ hybridization (ISH) and quantitative real-time PCR (qPCR) assays were developed to address this pressing need, and we provided an advance in the detection methods available. Pathogens can be seen in situ with associated lesions using ISH. Positive hybridization signals were noted inside the epithelial cells of the hepatopancreas, and putative free parasite spores were observed within the tubule lumen, which were associated with lesions detected by electron microscopy and haematoxylin and eosin (H&E) analysis. qPCR allows the determination of parasite loads in infected tissues, which is important for understanding disease progression and transmission. The hepatopancreas displayed the biggest statistical copy numbers among different tissues of infected crabs, confirming a tissue-specific pathogen infection characteristic. The qPCR assay also proved to be suitable for the diagnosis of asymptomatic carrier crabs. Combination of the two methods could facilitate the study of H. eriocheir infection mechanism in E. sinensis, enhance the early diagnosis of the pathogen and improve the management of microsporidian diseases in commercial crustaceans.

Parahepatospora carcini n. gen., n. sp., a parasite of invasive Carcinus maenas with intermediate features of sporogony between the Enterocytozoon clade and other microsporidia

Parahepatospora carcini n. gen. n. sp., is a novel microsporidian parasite discovered infecting the cytoplasm of epithelial cells of the hepatopancreas of a single Carcinus maenas specimen. The crab was sampled from within its invasive range in Atlantic Canada (Nova Scotia). Histopathology and transmission electron microscopy were used to show the development of the parasite within a simple interfacial membrane, culminating in the formation of unikaryotic spores with 5-6 turns of an isofilar polar filament. Formation of a multinucleate meront (>12 nuclei observed) preceded thickening and invagination of the plasmodial membrane, and in many cases, formation of spore extrusion precursors (polar filaments, anchoring disk) prior to complete separation of pre-sporoblasts from the sporogonial plasmodium. This developmental feature is intermediate between the Enterocytozoonidae (formation of spore extrusion precursors within the sporont plasmodium) and all other Microsporidia (formation of spore extrusion precursors after separation of sporont from the sporont plasmodium). SSU rRNA-based gene phylogenies place P. carcini within microsporidian Clade IV, between the Enterocytozoonidae and the so-called Enterocytospora-clade, which includes Enterocytospora artemiae and Globulispora mitoportans. Both of these groups contain gut-infecting microsporidians of aquatic invertebrates, fish and humans. According to morphological and phylogenetic characters, we propose that P. carcini occupies a basal position to the Enterocytozoonidae. We discuss the discovery of this parasite from a taxonomic perspective and consider its origins and presence within a high profile invasive host on the Atlantic Canadian coastline.

First case of hepatopancreatic necrosis disease in pond-reared Chinese mitten crab, Eriocheir sinensis, associated with microsporidian

An epidemic of hepatopancreatic necrosis disease (HPND) with a high mortality rate (40%-50%) recently occurred in the cultured Chinese mitten crab, Eriocheir sinensis, which is a very important economic crustacean species in China. Histology revealed infection by a microsporidian parasite within the cytoplasm of the epithelial cells of the hepatopancreas. Numerous discrete inclusions in the infected cells and presumably free parasite spores were also observed. By negative staining using electron microscopy, a typical morphology of spores was observed with a protuberant front of the anchoring disc. Infection was confined to the epithelial cells of the hepatopancreas, with no other organ implicated. By sequencing the PCR products using specific primers based on conserved regions of microsporidian small subunit (18S) ribosomal DNA, it was revealed that the parasite from HPND ponds had 99% sequence identity to that of Hepatospora eriocheir. Phylogentic analysis also placed the microsporidian in the same lineage as H. eriocheir. This study reported the first case of widespread infections of H. eriocheir associated with HPND found in the pond-reared Chinese mitten crab, E. sinensis. The description of microsporidian in this important commercial host is fundamental for future consideration of factors affecting stock health and sustainability.

Single and multi-gene phylogeny of Hepatospora (Microsporidia) - a generalist pathogen of farmed and wild crustacean hosts

Almost half of all known microsporidian taxa infect aquatic animals. Of these, many cause disease in arthropods. Hepatospora, a recently erected genus, infects epithelial cells of the hepatopancreas of wild and farmed decapod crustaceans. We isolated Hepatospora spp. from three different crustacean hosts, inhabiting different habitats and niches; marine edible crab (Cancer pagurus), estuarine and freshwater Chinese mitten crab (Eriocheir sinensis) and the marine mussel symbiont pea crab (Pinnotheres pisum). Isolates were initially compared using histology and electron microscopy revealing variation in size, polar filament arrangement and nuclear development. However, sequence analysis of the partial SSU rDNA gene could not distinguish between the isolates (~99% similarity). In an attempt to resolve the relationship between Hepatospora isolated from E. sinensis and C. pagurus, six additional gene sequences were mined from on-going unpublished genome projects (RNA polymerase, arginyl tRNA synthetase, prolyl tRNA synthetase, chitin synthase, beta tubulin and heat shock protein 70). Primers were designed based on the above gene sequences to analyse Hepatospora isolated from pea crab. Despite application of gene sequences to concatenated phylogenies, we were unable to discriminate Hepatospora isolates obtained from these hosts and concluded that they likely represent a single species or, at least subspecies thereof. In this instance, concatenated phylogenetic analysis supported the SSU-based phylogeny, and further, demonstrated that microsporidian taxonomies based upon morphology alone are unreliable, even at the level of the species. Our data, together with description of H. eriocheir in Asian crab farms, reveal a preponderance for microvariants of this parasite to infect the gut of a wide array of decapods crustacean hosts and the potential for Hepatospora to exist as a cline across wide geographies and habitats.

A new microsporidium, Triwangia caridinae gen. nov., sp. nov. parasitizing fresh water shrimp, Caridina formosae (Decapoda: Atyidae) in Taiwan

A new microsporidium was isolated from the endemic, Taiwanese shrimp, Caridina formosae (Decapoda, Atyidae) from northern Taiwan. A conspicuous symptom of infection was presence of opaque white xenomas located in the proximity of the alimentary tract, the surface of the hepatopancreas, and the gills. A fully developed xenoma consisted of a hard, thick capsule filled with sporophorous vesicles containing multiple spores. Microsporidia developed synchronously within the same sporophorous vesicle, although the stage of parasite development differed among the vesicles. Fresh spores were pyriform, mononucleated and measured 6.53 × 4.38 μm. The polar filament was anisofilar with 9-11 coils. Phylogenetic analysis based on the small subunit ribosomal DNA sequence showed that the isolate is most similar to the fish microsporidian clade containing the genera Kabatana, Microgemma, Potaspora, Spraguea, and Teramicra. The highest sequence identity, 80%, was with Spraguea spp. Based on pathogenesis, life cycle and phylogenetic analysis, we erect a new genus and species, Triwangia caridinae for the novel microsporidium.

Enterocytozoon hepatopenaei sp. nov. (Microsporida: Enterocytozoonidae), a parasite of the black tiger shrimp Penaeus monodon (Decapoda: Penaeidae): Fine structure and phylogenetic relationships

A new microsporidian species, Enterocytozoon hepatopenaei sp. nov., is described from the hepatopancreas of the black tiger shrimp Penaeus monodon (Crustacea: Decapoda). Different stages of the parasite are described, from early sporogonal plasmodia to mature spores in the cytoplasm of host-cells. The multinucleate sporogonal plasmodia existed in direct contact with the host-cell cytoplasm and contained numerous small blebs at the surface. Binary fission of the plasmodial nuclei occurred during early plasmodial development and numerous pre-sporoblasts were formed within the plasmodium. Electron-dense disks and precursors of the polar tubule developed in the cytoplasm of the plasmodium prior to budding of early sporoblasts from the plasmodial surface. Mature spores were oval, measuring 0.7x1.1microm and contained a single nucleus, 5-6 coils of the polar filament, a posterior vacuole, an anchoring disk attached to the polar filament, and a thick electron-dense wall. The wall was composed of a plasmalemma, an electron-lucent endospore (10nm) and an electron-dense exospore (2nm). DNA primers designed from microsporidian SSU rRNA were used to amplify an 848bp product from the parasite genome (GenBank FJ496356). The sequenced product had 84% identity to the matching region of SSU rRNA from Enterocytozoon bieneusi. Based upon ultrastructural features unique to the family Enterocytozoonidae, cytoplasmic location of the plasmodia and SSU rRNA sequence identity 16% different from E. bieneusi, the parasite was considered to be a new species, E. hepatopenaei, within the genus Enterocytozoon.