Comparative transcriptome analysis reveals the gene expression profiling in bighead carp (Aristichthys nobilis) in response to acute nitrite toxicity

Chemical-defensome and whole-transcriptome expression of the silverside fish Basilichthys microlepidotus in response to chronic pollution in the Maipo River basin, Central Chile

Pollution is a major global concern affecting biodiversity, particularly of freshwater species. Populations have developed mechanisms to deal with pollution, such as the chemical defensome, which is a set of genes involved in maintaining internal stability. Pollution significantly affects the Maipo River basin in Chile. This area is home to the endemic silverside fish Basilichthys microlepidotus, whose populations are affected by pollution to different degrees. We assessed gene expression in the liver and gill of this species, focusing on whole-transcriptome and chemical-defensome levels, to identify both independent and shared mechanisms in response to pollution. The results showed that 14-18 genes were consistently expressed differently among populations in polluted areas. These genes were primarily involved in liver cell mitosis and in responses to organic chemicals and carcinogenic processes. Genes expressed differently in the gill were more abundant in immune system biological processes. All populations consistently downregulated chemical-defensome genes in the liver. In differentially expressed chemical-defensome genes, shared biological processes included virus response, cellular redox homeostasis and transport, organic cyclic compound response and DNA-templated transcription regulation. Studying chemical-defensome genes can help reveal common ways that pollution builds up over time, and examining the whole transcriptome can elucidate the context in which this response develops.

Key Factors Affecting the Flesh Flavor Quality and the Nutritional Value of Grass Carp in Four Culture Modes

Flavor and nutritional value are important qualities of freshwater fish products, but the key factors affecting these quality parameters remain unclear. In this study, four typical aquaculture modes, including the commercial feed treatment (control), faba bean treatment (FBT), grass powder treatment (GPT), and waving water treatment with commercial feed (WWT), were used to explore the regulatory effect of water quality and feed (eaten and uneaten) on the flesh flavor and nutrition in grass carp (Ctenopharyngodon idella), a freshwater fish of the largest global production. During the culture period (90 days), water quality parameters of the four modes were measured every 15 days, and the flavor quality was evaluated by volatile flavor compounds detection and electronic nose analyzer. Flesh crude protein, crude fat, free fatty acid and free amino acid profiles were also determined. The results showed that, in the late period, the FBT mode had the poorest water quality with highest concentrations of nitrite and nitrate, while the GPT mode has the best water quality among the four modes. Most flesh flavor compounds found in the flesh of the control, GPT and WWT modes were pleasant. In the FBT mode with the poorest water quality, on the other hand, we found lower flavor quality (higher contribution of fishy compounds), higher water content, and lower contents of crude protein, crude fat, free fatty acids and free amino acids, compared to the other three modes. Correlation analyses showed that nitrite and nitrate are probably key water quality factors affecting the flavor quality and nutritional values besides eaten feed and uneaten feed factors. This study can serve as an important reference for ecological regulation and feeding administration of flesh quality in freshwater aquaculture fish.

Transcriptome analysis reveals molecular mechanisms responsive to acute cold stress in the tropical stenothermal fish tiger barb (Puntius tetrazona)

BACKGROUND

Tropical stenothermal fish exhibit special tolerance and response to cold stress. However current knowledge of the molecular mechanisms response to cold stress in aquatic ectotherms is largely drawn from eurythermal or extreme stenothermal species. The tiger barb Puntius tetrazona is a tropical stenothermal fish, with great popularity in aquarium trade and research.

RESULTS

To investigate the response mechanism of P. tetrazona to low temperature, fish were exposed to increasing levels of acute cold stress. Histopathological analysis showed that the brain, gill, liver and muscle tissues appeared serious damage after cold stress (13 °C). Brain, gill, liver and muscle tissues from control (CTRL) groups (27 °C) and COLD stress groups (13 °C) of eight-month fish (gender-neutral) were sampled and assessed for transcriptomic profiling by high-throughput sequencing. 83.0 Gb of raw data were generated, filtered and assembled for de novo transcriptome assembly. According to the transcriptome reference, we obtained 392,878 transcripts and 238,878 unigenes, of which 89.29% of the latter were annotated. There were 23,743 differently expressed genes (DEGs) been filtered from four pairs of tissues (brain, gill, liver and muscle) between these cold stress and control groups. These DEGs were mainly involved in circadian entrainment, circadian rhythm, biosynthesis of steroid and fatty acid. There were 64 shared DEGs between the four pairs of groups, and five were related to ubiquitylation/deubiquitylation. Our results suggested that ubiquitin-mediated protein degradation might be necessary for tropical stenothermal fish coping with acute cold stress. Also, the significant cold-induced expression of heat shock 70 kDa protein (HSP70) and cold-induced RNA-binding protein (CIRBP) was verified. These results suggested that the expression of the molecular chaperones HSP70 and CIRBP in P. tetrazona might play a critical role in coping with acute cold stress.

CONCLUSIONS

This is the first transcriptome analysis of P. tetrazona using RNA-Seq technology. Novel findings about tropical stenothermal fish under cold stress (such as HSP70 and CIRBP genes) are presented here. This study contributes new insights into the molecular mechanisms of tropical stenothermal species response to acute cold stress.

Comparative transcriptome analyses and identification of candidate genes involved in vertebral abnormality of bighead carp Hypophthalmichthys nobilis

Body deformity occurs both in wild and farmed fishes, which is one of the most challenging problems for aquaculture industry. In most cases, such body deformities are linked to skeletal deformities. Currently, very limited information is available on skeletal deformities of farmed fish species which may be caused by genetic factor. In this study, we performed muscle and vertebra transcriptome analyses in body deformity and normality of bighead carp Hypophthalmichthys nobilis (from one meiotic gynogenesis family) using RNA-Seq. A total of 43,923 and 44,416 unigenes were predicted in muscles and vertebrae, respectively. Based on these data, we further explored the gene expression profiles in gynogenetic normal and abnormal bighead carp. No differentially expressed gene (DEG) was found in transcriptome data of muscles. Totally, 20 key DEGs were identified in transcriptome data of vertebrae, such as low density lipoprotein-related protein 2 (lrp2), bone morphogenetic protein 2B (bmp2b) and collagen alpha-1(IV) (col4a1). 12 potential pathways were also identified in vertebra transcriptome data, which were mainly involved in development, growth, cytoskeleton and energy metabolism, such as MAPK signaling pathway, regulation of actin cytoskeleton and TGF-beta signaling pathway. Results of this study will be informative for the understanding of genetic mechanisms for body shape formation and also provide potential candidate genes for selection program involved in body shape and skeletal development in H. nobilis.

The regulation of the disease resistance, mTOR and NF-kB signaling pathway of Aristichthys nobilis using Rhodopseudomonas wastewater treatment

The employment of traditional feed and medicament in freshwater aquaculture causes the frequent occurrence of environmental pollution and disease. Effluent collected after Rhodopseudomonas-mediated wastewater treatment could be re-utilized as microbial feeds, and aquaculture water to culture Aristichthys nobilis. Therefore, a novel integrated system of wastewater treatment using effluent containing Rhodopseudomonas that improves yield, increases disease resistance, and enhances the quality of aquaculture water for Aristichthys nobilis culture was proposed and investigated. Aristichthys nobilis can grow well in effluent containing Rhodopseudomonas (ER). The survival rate, yield, and whole body composition of the ER group were all increased compared to the control group (CK). The biochemical (B vitamin) and other substances in the effluent of Rhodopseudomonas enhanced the activity of AKP, ACP, phagocytic, SOD, and CAT by upregulating the expression of AKP, ACP, SOD, and CAT genes. Moreover, Rhodopseudomonas and biochemical substances improved mTOR and NF-kB signaling pathway. Furthermore, Rhodopseudomonas inhibited Aeromonas hydrophila that increases resistance against fish disease. Meanwhile, Rhodopseudomonas in the effluent also improved the aquaculture water quality. This technology would save the aquaculture water, reduce water pollution and wastewater discharge, and increase the output and disease resistance of Aristichthys nobilis, simultaneously.

Acute Exposure to key Aquaculture Environmental Stressors Impaired the Aerobic Metabolism of Carassius auratus gibelio

Carassius auratus gibelio is an omnivore favored for its flavor and is commonly used as a benthic species in traditional pond polyculture. This study investigated the effects of common aquaculture stressors, such as high ammonia, high nitrite, high pH, and hypoxia on the aerobic metabolism of C. auratus gibelio. The results showed that the standard metabolic rate (SMR) was positively correlated with ammonia, nitrite, and pH, while the maximum metabolic rate (MMR) was negatively correlated with all four stressors. Thus, aerobic scope (AS) was reduced when C. auratus gibelio was exposed to high ammonia, high nitrite, high pH, and hypoxia. The peak of post-prandial O₂ consumption was positively correlated with nitrite, pH, and the occurrence of the peak metabolic rate post-prandial was delayed in high ammonia, high nitrite, hypoxia, and high pH conditions. These findings indicated that, in experimental conditions, exposure to these environmental stressors can influence aerobic metabolism in C. auratus gibelio. With more energy required to maintain standard metabolic rates, less will be available for growth. While the C. auratus gibelio is one of the most hypoxia tolerance species, the reduction we observed in AS caused by stressors that commonly occur in ponds and in nature will likely affect growth in ponds and fitness in nature. These data have provided insight into the optimal, fitness-maximizing thresholds for these common stressors in this species of interest.

Toxic effects of waterborne nitrite exposure on antioxidant responses, acetylcholinesterase inhibition, and immune responses in olive flounders, Paralichthys olivaceus, reared in bio-floc and seawater

Paralichthys olivaceus (mean weight, 280.1 ± 10.5 g; mean length, 28.37 ± 2.3 cm) was reared in bio-floc and seawater for 6 months to determine the toxic effects of waterborne nitrite exposure (0, 25, 50, 100, and 200 mg/L) for 1 week, compared to those observed with bio-floc and seawater only. The effects on antioxidant activity, immune responses, and acetylcholinesterase activity were measured. Following nitrite exposure, superoxide dismutase activity in the liver and gills was significantly elevated and catalase activity was significantly increased, except for in the gills of P. olivaceus reared in bio-floc. Further, glutathione S-transferase activity was significantly elevated in the liver and gills, and glutathione was significantly lower. Meanwhile, acetylcholinesterase activity in the liver and gills was significantly inhibited and plasma lysozyme activity and immunoglobulin M were considerably elevated.

Inorganic nitrite increases the susceptibility of tilapia (Oreochromis niloticus) leucocytes to Streptococcus agalactiae

Deteriorating water quality, especially from high concentrations of nitrite, is currently largely blamed for disease outbreaks in farmed tilapia (Oreochromis niloticus). In this study, the underlying mechanism of nitrite on the susceptibility of tilapia leucocytes to Streptococcus agalactiae (S. agalactiae) was studied. We found that a high dose of heat-killed S. agalactiae decreased tilapia leucocytes cell viability, whereas nitrite decreased the cell viability of leucocytes exposed to a low dose of bacteria. Bacterial challenge increased the production of nitric oxide (NO), whereas nitrite and bacteria coexposure caused higher NO production than nitrite or bacterial exposure alone. Cell viability increased after elimination of NO, and negative correlations existed between cell viability and the NO content, suggesting that nitrite increased the susceptibility of the leucocytes against S. agalactiae was NO-dependent. For a more comprehensive understanding of the mechanism of nitrite affecting disease resistance in tilapia leucocytes, an RNA-Seq-based transcriptome was generated. The results showed that 6173 transcripts were differently expressed, and the differentially expressed transcripts (DETs) of the bacterial group, nitrite group and bacteria-nitrite co-treatment group compared to the control group were selected for GO and KEGG analyses. The DETs in the bacterial group and bacteria-nitrite cotreatment group were highly involved with the membrane component, signal transduction, and immune responses. KEGG analysis showed that the protein processing in the endoplasmic reticulum and the AMPK signaling pathway, which are related to autophagy, were significantly enriched in the cotreatment group but not in bacterial group. In addition, the mRNA expression of ten DETs and several autophagy and apoptosis related genes validated by q-PCR showed the high reliability of the RNA-seq. Taken together, the results of this study suggest that nitrite may increase the susceptibility of tilapia leucocytes to S. agalactiae by generating excess NO to affect the autophagy and apoptosis process.

Impact of nitrite exposure on plasma biochemical parameters and immune-related responses in Takifugu rubripes

Nitrite is a major environmental pollutant in aquatic environments that negatively affects aquatic species. In this study, we investigated the impact of nitrite exposure on plasma biochemical parameters and immune responses in Takifugu rubripes. Fish were exposed to various concentrations of nitrite (0, 0.5, 1, 3, and 6 mM) for 96 h. After 0, 12, 24, 48, and 96 h of exposure, fish blood samples were collected to assay the levels of total protein (TP), albumin (Alb), glutamic-oxaloacetic transaminase (GOT), glutamic-pyruvic transaminase (ALT), complement C3 (C3), complement C4 (C4), immunoglobulin (IgM), and lysozyme activity (LZM). The gills were sampled to analyze the mRNA levels of heat shock protein 70 (hsp70), heat shock protein 90 (hsp90), tumor necrosis factor α (tnf-α), B-cell activating factor (baff), interleukin-6 (il-6), and interleukin-12 (il-12). Levels of GOT, ALT, C3, and C4 were significantly enhanced in the high nitrite concentration group (3 and 6 mM), whereas those of TP, Alb, LZM, and IgM decreased significantly with the same treatments. Nitrite significantly upregulated hsp70, hsp90, tnf-α, il-6, il-12, and baff mRNA levels after 96 h of exposure. These results indicated that nitrite exposure altered the blood physiological status and immune system response, resulting in dysfunction and immunotoxicity in T. rubripes. Furthermore, our results reveal the possible mechanism of aquatic-nitrite-induced toxicity in fish.

Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis)

BACKGROUND

Early development is a key process of the life history of fish. However, the relationship between the transcriptome and the dynamic regulation of early development is still uncharacterized in the bighead carp (Hypophthalmichthys nobilis). In the present study, we performed transcriptome analysis of six development stages in H. nobilis, aiming to understand the dynamic molecular regulation of early development in this fish.

RESULTS

A total of 76,573 unigenes were assembled from clean sequence reads, with an average length of 1768 base. Among which, 41,742 (54.54%) unigenes were annotated to public protein databases, and an additional 59,014 simple sequence repeat (SSR) loci were identified among the unigenes. Furthermore, 30,199 differentially expressed transcripts (DETs) (fold change > 4 or < 0.25, and the false discovery rate FDR < 0.01) were observed in comparisons between the adjacent developmental stages, and nine expression patterns (profiles) were simulated using series-cluster analysis across six developmental stages. The unigenes expression level markedly increased after the DS1 stage (early blastula), and the numbers of DETs gradually decreased during subsequent development. The largest transcriptomic change (up- or down-regulated) was detected during the period from DS1 to DS2 (6-somite stage), which was enriched for many biological processes and metabolic pathways related to maternal to zygotic transition (MZT). Distinctly protein-protein interaction (PPI) networks were plotted for DETs during the period from DS1 to DS2. The genes (or proteins) from the same pathways were integrated together, and showed with obvious co-regulation patterns. In the series-cluster analysis, a remarkable profile of gene expression (profile_48) was identified that is probably related to the hatching during H. nobilis development, and the strict co-expression of a hatching enzyme gene (hce1) with 33 other annotated genes was identified from this profile.

CONCLUSIONS

The results indicated that strict dynamic regulation occurs during the early development in H. nobilis, especially in embryogenesis before hatching. This study provides valuable new information and transcriptomic resources related to H. nobilis early development, and for certain events such as MZT and hatching.

Research on complexation ability, aromaticity, mobility and cytotoxicity of humic-like substances during degradation process by electrochemical oxidation

The humic-like substances were the main organic components in most wastewater (e.g. domestic sewage, toilet wastewater and landfill leachate). Two types of actual humic-like substances (fulvic acid (FA) and biologically treated landfill leachate (BTLL)) were selected to describe the changes in the properties of humic-like substances (complexation ability, aromaticity and mobility) during electrochemical oxidation. Meanwhile, the acute cytotoxicity of FA and BTLL was also tested by acute toxicological test of luminescent bacteria. The results showed that the consumption of coordinating groups such as phenolic groups and hydrogen bonds reduced the complexation ability of FA and BTLL. The functional groups were degraded with the removal order of quinone group, phenolic group and aromatic group, and finally realized the molecular saturation and aromaticity decrease for humic-like substances. The mobility of FA and BTLL was decreased because of the enhancement of hydrophobicity during electrolysis process. Furthermore, the available chlorine produced during electrochemical oxidation was the main acute cytotoxicity substance, therefore, it is necessary to remove it before discharge in order to reduce ecological risks. This study provides a basis for understanding and evaluating the electrochemical degradation process of humic-like substances in detail.

Serum biochemistry, liver histology and transcriptome profiling of bighead carp Aristichthys nobilis following different dietary protein levels

Dietary protein plays a major role in determining the rate of fish growth and overall health. Given that the liver is an important organ for metabolism and detoxification, we hypothesized that optimal dietary protein levels may benefit liver function. Herein, we investigated the effects of dietary protein level on serum biochemistry, liver histology and transcriptome profiling of juvenile bighead carp Aristichthys nobilis fed for 8 weeks on a diet supplemented with high protein (HP, 40%), low protein (LP, 24%) or optimal protein (OP, 32%; controls). The results revealed a significant change in liver morphology in LP and HP groups compared with the OP group, coupled with increased serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT) activity. RNA sequencing (RNA-Seq) analysis of the liver transcriptome yielded 47 million high-quality reads using an Illumina platform, which were de novo assembled into 80,777 unique transcript fragments (unigenes) with an average length of 1021 bp. Subsequent bioinformatics analysis identified 878 and 733 differentially expressed unigenes (DEGs) in liver in response to LP and HP diets, respectively. KEGG enrichment analysis of DEGs identified immune and metabolism-related pathways, including Toll-like receptor signaling, PI3K-Akt signaling, NF-κB signaling, complement and coagulation, peroxisome, nitrogen metabolism, PPAR signaling, and glycolysis and gluconeogenesis pathways. Transcriptome profiling results were validated by quantitative real-time PCR for 16 selected DEGs. The findings expand our understanding of the molecular mechanisms underlying the effects of dietary protein level on liver function in bighead carp.

Characterization of transcriptional responses mediated by benzo[a]pyrene stress in a new marine fish model of goby, Mugilogobius chulae

Benzo[a]pyrene (BaP) is one of the most studied targets among polycyclic aromatic hydrocarbons (PAHs). Because of the complexity of the toxicity mechanism in BaP, little is known about the molecular mechanism at the level of transcription of BaP in marine fishes. The primary objective of this study was to investigate the molecular basis of the effects of BaP on marine fish, using Mugilogobius chulae (Smith 1932) as the model. A closed colony of M. chulae was used for the BaP toxicity test. Two fish liver samples per replicate from each group were excised and blended into one sample by pooling an equal amount of liver tissue. Total RNA of all samples was extracted separately. Equal quantities of total RNA from the three replicates of the two groups were pooled for sequencing. The sequencing cDNA libraries were sequenced using Illumina HiSeq 2000 system. Differentially expressed genes were detected with the DEGSeq R package. In total, 52,364,032 and 53,771,748 clean nucleotide reads were obtained in the control and BaP-exposed libraries, respectively, with N50 lengths of 1277 and 1288 bp, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed a significant enrichment of genes related to detoxification, transportation, and lipid metabolism. We also identified, for the first time, an association between endoplasmic reticulum dysfunction and lipid metabolism resulting from BaP exposure. Using quantitative real-time PCR, some effective molecular biomarkers for monitoring of BaP-polluted seawater were identified. The results demonstrate that BaP enhanced the expression of genes involved in detoxification in M. chulae and inhibited that of genes related to lipid metabolism, possibly by suppressing the expression of numerous ER-related genes involved in fat digestion and absorption.