Transcriptome analysis of goldfish (Carassius auratus) in response to Gyrodactylus kobayashii infection

Transcriptomic analysis of immune-related genes in Pacific white snook (Centropomus viridis) gills infected with the monogenean parasite Rhabdosynochus viridisi

The parasite Rhabdosynochus viridisi (Platyhelminthes: Monogenea) infects the Pacific white snook Centropomus viridis gills and can cause adverse effects in the aquaculture industry. The immune responses of Pacific white snook to monogenean infections are poorly understood. Thus, this study aimed to identify differentially expressed genes (DEGs) in the gills of Pacific white snook juveniles experimentally infected with R. viridisi, emphasizing immune-related genes and pathways activated or suppressed during the infection. RNA sequencing was performed on the gills of uninfected (control) and infected fish. The algorithm Seq2Fun was selected without a reference transcriptome to map the reads to transcripts of fishes available from a database for gene orthologs (EcoOmics) and obtain the counting table. The ExpressAnalyst software was used for differential expression and functional analyses. A total of 20,106 transcripts were found, and 1430 (7 %) were differentially expressed genes (DEGs) between infected and control groups. We identified 860 (60 %) downregulated and 570 (40 %) upregulated genes. Thirteen canonical pathways after the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were overrepresented, and most of the DEGs were downregulated, suggesting the inactivation of these pathways. The functions of most of the DEGs with higher fold change found in this study are poorly understood in fish. Even though the well-known pro-inflammatory cytokines remained unchanged in infected gills of C. viridis, and transforming growth factor β (tgfβ) was downregulated, interleukin-17 ligands il17d and il17a/f1, as well as C-X-C motif chemokine receptor 2 (cxcr2) genes were upregulated, indicating that the infection with R. viridisi promotes Th17-like immunity. Overexpression of plasma B cell activity markers such as immunoglobulin light chain-like genes and the v-set pre-B cell surrogate light chain 3 (vpreb3) was also detected in this study. The possible implications of DEGs related to calcium imbalance, hypoxia adaptation, hemostasis, and immunity are discussed. These results will support future studies to improve the prevention and treatment of monogenean infections in finfish aquaculture.

Genetic improvement and genomic resources of important cyprinid species: status and future perspectives for sustainable production

Cyprinid species are the most cultured aquatic species around the world in terms of quantity and total value. They account for 25% of global aquaculture production and significantly contribute to fulfilling the demand for fish food. The aquaculture of these species is facing severe concerns in terms of seed quality, rising feed costs, disease outbreaks, introgression of exotic species, environmental impacts, and anthropogenic activities. Numerous researchers have explored biological issues and potential methods to enhance cyprinid aquaculture. Selective breeding is extensively employed in cyprinid species to enhance specific traits like growth and disease resistance. In this context, we have discussed the efforts made to improve important cyprinid aquaculture practices through genetic and genomic approaches. The recent advances in DNA sequencing technologies and genomic tools have revolutionized the understanding of biological research. The generation of a complete genome and other genomic resources in cyprinid species has significantly strengthened molecular-level investigations into disease resistance, growth, reproduction, and adaptation to changing environments. We conducted a comprehensive review of genomic research in important cyprinid species, encompassing genome, transcriptome, proteome, metagenome, epigenome, etc. This review reveals that considerable data has been generated for cyprinid species. However, the seamless integration of this valuable data into genetic selection programs has yet to be achieved. In the upcoming years, genomic techniques, gene transfer, genome editing tools are expected to bring a paradigm shift in sustainable cyprinid aquaculture production. The comprehensive information presented here will offer insights for the cyprinid aquaculture research community.

Anthelmintic efficacy of febantel against a monogenean parasite, Gyrodactylus kobayashii

Monogenean parasites pose a significant challenge to aquaculture, leading to adverse effects on fish health and yields. Current anthelmintic treatments for monogeneans have demonstrated limited efficacy and are further complicated by potential issues, which emphasize the necessity for effective and safe therapeutic strategies to manage monogeneans in aquaculture. In this study, in vivo and in vitro anthelmintic activity of febantel against Gyrodactylus kobayashii on goldfish (Carassius auratus), as well as its toxicity to goldfish were evaluated. In vivo assays indicated that febantel exhibited potent anthelmintic activity against G. kobayashii with an EC50 value of 0.03 mg/L and 100 % anthelmintic efficacy at 0.1 mg/L after 48 h of exposure. Moreover, in vivo trials also revealed a notable post-treatment effect of febantel, where infected goldfish transferred to drug-free water after short 6-h exposure could still result in full eradication of the worms, indicating febantel might induce persistent perturbations in parasite physiology. In vitro assays showed a negative correlation between febantel concentrations and the survival of G. kobayashii. However, increasing the febantel concentration to 2.0 mg/L did not result in the complete death of all worms. Oral administration of febantel demonstrated limited anthelmintic activity, with only 49 % efficacy at a dosage of 200 mg/kg body weight daily over five days. Acute toxicity assays revealed the 48-h LC50 value of febantel was 5.47 mg/L, which was 182.23 times higher than the 48-h EC50 value, indicating that febantel has a favorable safety profile. However, febantel exposure potentially interfered with hepatic metabolism and oxidative status, as indicated by variations in SOD, GST, and P450 gene expression. In conclusion, treatment with 0.1 mg/L febantel for 24 h completely eradicated G. kobayashii infection on goldfish, demonstrating febantel's potent anthelmintic activity. Coupled with its safety profile and extended post-treatment effectiveness, febantel is a promising candidate for controlling Gyrodactylus infections in aquaculture.

Transcriptome Profile Analyses of Head Kidney in Roach (Rutilus rutilus), Common Bream (Abramis brama) and Their Hybrids: Does Infection by Monogenean Parasites in Freshwater Fish Reveal Differences in Fish Vigour among Parental Species and Their Hybrids?

Hybrid generations usually face either a heterosis advantage or a breakdown, that can be expressed by the level of parasite infection in hybrid hosts. Hybrids are less infected by parasites than parental species (especially F1 generations) or more infected than parental species (especially post-F1 generations). We performed the experiment with blood-feeding gill parasite Paradiplozoon homoion (Monogenea) infecting leuciscid species, Abramis brama and Rutilus rutilus, their F1 generation and two backcross generations. Backcross generations tended to be more parasitized than parental lines and the F1 generation. The number of differentially expressed genes (DEGs) was lower in F1 hybrids and higher in backcross hybrids when compared to each of the parental lines. The main groups of DEGs were shared among lines; however, A. brama and R. rutilus differed in some of the top gene ontology (GO) terms. DEG analyses revealed the role of heme binding and erythrocyte differentiation after infection by blood-feeding P. homoion. Two backcross generations shared some of the top GO terms, representing mostly downregulated genes associated with P. homoion infection. KEGG analysis revealed the importance of disease-associated pathways; the majority of them were shared by two backcross generations. Our study revealed the most pronounced DEGs associated with blood-feeding monogeneans in backcross hybrids, potentially (but not exclusively) explainable by hybrid breakdown. The lower DEGs reported in F1 hybrids being less parasitized than backcross hybrids is in line with the hybrid advantage.

Effect of Copper Sulphate Exposure on the Oxidative Stress, Gill Transcriptome and External Microbiota of Yellow Catfish, Pelteobagrus fulvidraco

This study aimed to investigate the potential adverse effects of the practical application of copper sulfate on yellow catfish (Pelteobagrus fulvidraco) and to provide insights into the gill toxicity induced by copper sulphate. Yellow catfish were exposed to a conventional anthelmintic concentration of copper sulphate (0.7 mg/L) for seven days. Oxidative stress biomarkers, transcriptome, and external microbiota of gills were examined using enzymatic assays, RNA-sequencing, and 16S rDNA analysis, respectively. Copper sulphate exposure led to oxidative stress and immunosuppression in the gills, with increased levels of oxidative stress biomarkers and altered expression of immune-related differentially expressed genes (DEGs), such as IL-1β, IL4Rα, and CCL24. Key pathways involved in the response included cytokine-cytokine receptor interaction, NOD-like receptor signaling pathway, and Toll-like receptor signaling pathway. The 16S rDNA analysis revealed copper sulphate altered the diversity and composition of gill microbiota, as evidenced by a significant decrease in the abundance of Bacteroidotas and Bdellovibrionota and a significant increase in the abundance of Proteobacteria. Notably, a substantial 8.5-fold increase in the abundance of Plesiomonas was also observed at the genus level. Our findings demonstrated that copper sulphate induced oxidative stress, immunosuppression, and gill microflora dysbiosis in yellow catfish. These findings highlight the need for sustainable management practices and alternative therapeutic strategies in the aquaculture industry to mitigate the adverse effects of copper sulphate on fish and other aquatic organisms.

Effects of nanoplastic exposure on the immunity and metabolism of red crayfish (Cherax quadricarinatus) based on high-throughput sequencing

Previous studies have shown that nanoplastics (NPs) are harmful pollutants that threaten aquatic organisms and ecosystems, however, less research has been conducted on the hazards of NPs for aquaculture animals. In this study, Cherax quadricarinatus was used as an experimental model to evaluate the possible effects of three concentrations (25, 250 and 2500 μg/L) of NPs on red crayfish. The toxicological effects of NPs on this species were investigated based on transcriptomics and microbiome. A total of 67,668 genes were obtained from the transcriptome. The annotation rate of the four major libraries (Nr, KEGG, KOG, Swissprot) was 40.17 %, and the functions of differential genes were mainly related to antioxidant activity, metabolism and immune processes. During the experiment, the activities of superoxide dismutase (SOD) and catalase (CAT) in the high concentration group were significantly decreased, while the concentration of malondialdehyde (MDA) increased after nanoplastics (NPs) exposure, and SOD1, Jafrac1 were significantly reduced at high concentrations. expression is inhibited. The immune genes LYZ and PPO2 were highly expressed at low concentrations and suppressed at high concentrations. After 14 days of exposure to NPs, significant changes in gut microbiota were observed, such as decreased abundances of Actinobacteria, Bacteroidetes, and Firmicutes. NPs compromise host health by inducing changes in microbial communities and the production of beneficial bacterial metabolites. Overall, these results suggest that NPs affect immune-related gene expression and antioxidant enzyme activity in red crayfish and cause redox imbalance in the body, altering the composition and diversity of the gut microbiota.

Infection by the Parasite Myxobolus bejeranoi (Cnidaria: Myxozoa) Suppresses the Immune System of Hybrid Tilapia

Myxozoa (Cnidaria) is a large group of microscopic obligate endoparasites that can cause emerging diseases, affecting wild fish populations and fisheries. Recently, the myxozoan Myxobolus bejeranoi was found to infect the gills of hybrid tilapia (Nile tilapia (Oreochromis niloticus) × Jordan/blue tilapia (O. aureus)), causing high morbidity and mortality. Here, we used comparative transcriptomics to elucidate the molecular processes occurring in the fish host following infection by M. bejeranoi. Fish were exposed to pond water containing actinospores for 24 h and the effects of minor, intermediate, and severe infections on the sporulation site, the gills, and on the hematopoietic organs, head kidney and spleen, were compared. Enrichment analysis for GO and KEGG pathways indicated immune system activation in gills at severe infection, whereas in the head kidney a broad immune suppression included deactivation of cytokines and GATA3 transcription factor responsible for T helper cell differentiation. In the spleen, the cytotoxic effector proteins perforin and granzyme B were downregulated and insulin, which may function as an immunomodulatory hormone inducing systemic immune suppression, was upregulated. These findings suggest that M. bejeranoi is a highly efficient parasite that disables the defense mechanisms of its fish host hybrid tilapia.

Transport stress induces innate immunity responses through TLR and NLR signaling pathways and increases mucus cell number in gills of hybrid yellow catfish (Tachysurus fulvidraco ♀ × Pseudobagrus vachellii ♂)

Transport stress poses a threat to most teleost fish in production, causing mass losses to the aquaculture industry. Fish gills are a mucosa-associated lymphoid tissue in direct contact with water, and they represent an ideal tissue type to study mechanisms of transport stress. In this study, hybrid yellow catfish (Tachysurus fulvidraco ♀ × Pseudobagrus vachellii ♂) were exposed to simulated transport stress for 16 h and then allowed to recover for 96 h. Gill tissues and blood samples were collected at 0 h, 2 h, 4 h, 8 h, and 16 h of transport stress and after 96 h of recovery, as well as from fish in a control group at the same sampling times. The activities of alkaline phosphatase, acid phosphatase, and superoxide dismutase and the total antioxidant capacity first increased and then decreased during the 16 h transport treatment. Exposure to 16 h of transport stress resulted in decreased serum triglyceride and total cholesterol contents, increased serum glucose content, increased activities of alanine aminotransferase and aspartate transaminase, and more mucus cells, compared with the control group. Transcriptome analysis revealed differential expression of 1525 genes (803 down-regulated and 722 up-regulated) between the control and 16 h transportation groups. Functional analyses revealed that the differentially expressed genes were enriched in immune response, signal transduction, and energy metabolism pathways. We found that tlr5, tnfɑ, hsp90ɑ, il-1ß, map2k4, il12ba were clearly up-regulated and arrdc2, syngr1a were clearly down-regulated following 8 h and/or 16 h simulated transport after qRT-PCR validation. These findings suggested that Toll- and NOD-like receptor signaling pathways potentially mediate transport stress. Transport stress altered innate immunity responses and energy use in the gill tissues of hybrid yellow catfish. After 96 h of recovery, only alanine aminotransferase and alkaline phosphatase activities and the number of mucus cells had returned to control levels. We speculate that for juvenile yellow catfish to recover to a normal state, a recovery period of more than 96 h is required after 16 h of transportation. These results provide new perspectives on the immune response of yellow catfish under transport stress and theoretical support for future optimization of their transportation.

Transmission dynamics of ectoparasitic gyrodactylids (Platyhelminthes, Monogenea): An integrative review

Parasite transmission is the ability of pathogens to move between hosts. As a key component of the interaction between hosts and parasites, it has crucial implications for the fitness of both. Here, we review the transmission dynamics of Gyrodactylus species, which are monogenean ectoparasites of teleost fishes and a prominent model for studies of parasite transmission. Particularly, we focus on the most studied host–parasite system within this genus: guppies, Poecilia reticulata, and G. turnbulli/G. bullatarudis. Through an integrative literature examination, we identify the main variables affecting Gyrodactylus spread between hosts, and the potential factors that enhance their transmission. Previous research indicates that Gyrodactylids spread when their current conditions are unsuitable. Transmission depends on abiotic factors like temperature, and biotic variables such as gyrodactylid biology, host heterogeneity, and their interaction. Variation in the degree of social contact between hosts and sexes might also result in distinct dynamics. Our review highlights a lack of mathematical models that could help predict the dynamics of gyrodactylids, and there is also a bias to study only a few species. Future research may usefully focus on how gyrodactylid reproductive traits and host heterogeneity promote transmission and should incorporate the feedbacks between host behaviour and parasite transmission.

Effects of acute deltamethrin exposure on kidney transcriptome and intestinal microbiota in goldfish (Carassius auratus)

As a widely used synthetic pyrethroid insecticide, deltamethrin (DM) causes serious health problems to aquatic organisms. However, the comprehensive understanding of the adverse effect of DM on aquatic organisms has received limited attention. In this study, goldfish (Carassius auratus) were exposed to 0 (control group), 0.2 and 2 µg/L DM for 96 h. The kidney transcriptome and intestinal microbiota were investigated. Comparative transcriptome analysis identified 270 and 711 differentially expressed genes (DEGs) in goldfish kidneys after exposure to 0.2 and 2 µg/L DM, respectively. KEGG pathway analysis revealed that the apoptosis pathway was markedly regulated and the regulation of programmed cell death was significantly enriched by the GO analysis. Several apoptosis-related genes including cathepsin L and cytochrome c were also detected. These results indicated that apoptosis occurred in the goldfish kidney after acute exposure to sublethal concentration of DM. Besides, some immune and drug metabolism-related DEGs were identified, indicating that exposure to DM caused immunotoxicity and metabolic disruption in goldfish. Additionally, 16 S rRNA gene sequencing analysis revealed a remarkable alteration in the composition of the intestinal microbial community of DM-treated goldfish. At the phylum level, the abundance of Proteobacteria, Firmicutes and Fusobacteria was increased, whereas the abundance of Bacteroidetes was reduced significantly after DM exposure. At the genus level, the abundance of Aeromonas, Cetobacterium, Dielma and Pseudorhodobacter was reduced, whereas Akkermansia was increased after DM exposure. In summary, exposure to DM could induce apoptosis and immunotoxicity in goldfish kidneys and affect the composition of the intestinal microbiota in goldfish. This study provides a comprehensive analysis of the adverse effect of DM exposure on the goldfish and will be helpful for understanding the toxicological mechanisms of DM in fish.

Climate change affects the parasitism rate and impairs the regulation of genes related to oxidative stress and ionoregulation of Colossoma macropomum

Global climate change represents a critical threat to the environment since it influences organismic interactions, such as the host-parasite systems, mainly in ectotherms including fishes. Rising temperature and CO₂ are predicted to affect this interaction other and critical physiological processes in fish. Herein, we investigated the effects of different periods of exposure to climate change scenarios and to two degrees of parasitism by monogeneans in the host-parasite interaction, as well as the antioxidant and ionoregulatory responses of tambaqui (Colossoma macropomum), an important species in South American fishing and aquaculture. We hypothesized that temperature and CO₂ changes in combination with parasite infection would interfere with the host's physiological processes that are related to oxidative stress and ionoregulation. We experimentally exposed C. macropomum to low and high levels of parasitism in the current and extreme climate scenarios (4.5 °C and 900 ppm CO₂ above current levels) for periods of seven and thirty days and we use as analyzed factors; the exposure time, the climate scenario and parasitism level in a 2 × 2 × 2 factorial through a three-way ANOVA as being fish the experimental unit (n = 8). An analysis of gill enzymatic and gene expression profile was performed to assess physiological (SOD, GPx and Na⁺/K⁺-ATPase enzymes) and molecular (Nrf2, SOD1, HIF-1α and NKA α1a genes) responses. A clear difference in the parasitism levels of individuals exposed to the extreme climate scenario was observed with a rapid and aggressive increase that was higher after 7 days of exposure though showed a decrease after 30 days. The combination of exposure to the extreme climate change scenario and parasitism caused oxidative stress and osmoregulatory disturbance, which was observed through the analysis of gene expression (Nrf2, SOD1, HIF-1α and NKA α1a) and antioxidant and ionoregulatory enzymes (SOD, GPx and Na⁺/K⁺-ATPase) on the host, possibly linked to inflammatory processes caused by the high degree of parasitism. In the coming years, these conditions may result in losses of performance for this species, and as such will represent ecological damage and economical losses, and result in a possible vulnerability in relation to food security.