Analysis of digital gene expression profiling in hemocytes of white shrimp Litopenaeus vannamei under nitrite stress

Trophic transfer and their impact of microplastics on estuarine food chain model

Microplastic contamination in marine ecosystems, and its negative effects through trophic transfer among marine organisms, remains a growing concern. Our study investigates the trophic transfer and individual impacts of polystyrene microplastics (MPs) in an estuarine food chain model, comprising Artemia salina as primary organism, Litopenaeus vanamei as secondary organism, and Oreochromis niloticus as tertiary organism. A. salina were exposed to 1 µm polystyrene microplastics (106 particles/ml), further it was fed to L.vannamei, which, in turn, were fed to O.niloticus. MPs transfer was studied over 24 and 48 h. Fluorescence microscopy confirmed MPs presence in the gut and fecal matter of all the test organisms. Histopathology revealed MPs in the gut epithelium, but did not translocate to other tissues of the test species. MPs exposed A.salina had a bioconcentration factor of 0.0029 ± 0.0008 (24 h) and 0.0000941 ± 0.0000721 (48 h). Whereas, the bioaccumulation factor values for L. vanamei were 0.00012143 ± 0.000009 (24 h) and 0.0025899 ± 0.0024101 (48 h), and for O.niloticus were 0.154992 ± 0.007695 (24 h) and 0.00972577 ± 0.00589923 (48 h). Despite low MPs transfer among trophic levels, the induced stress was evident through biochemical responses in all the test species. This implies the potential risk of MPs ultimately reaching humans via the food chain.

Growth, immunity and transcriptome response to different stocking densities in Litopenaeus vannamei

The effects of different stocking densities on Litopenaeus vannamei were investigated from the aspects of growth performance, immune response and transcriptome in this experiment. L. vannamei (initial body weight: 0.30 ± 0.02 g) were reared for 8 weeks at three stocking densities of 100 (LSD), 200 (MSD) and 300 (HSD) shrimp/m³, respectively. The results showed that the survival rate (SR), final body weight (FBW), weight gain rate (WGR), specific growth ratio (SGR) and protein efficiency ratio (PER) of L. vannamei significantly decreased, while the feed factor (FCR) significantly increased with the increase of stocking density. After Vibrio parahemolyticus infection, the SR of L. vannamei in the HSD group was significantly lower than that in the LSD and MSD groups. Increasing stocking density significantly increased the activities of aspartate aminotransferase (AST), alanine aminotransferase (ALT) and lysozyme (LYS) while significantly decreased the activities of catalase (CAT) and phenol oxidase (PO) in the serum of L. vannamei. Similar changes of the gene expression as the activities of immune enzymes were found in the hemocytes. Pairwise comparison between the LSD, MSD and HSD group in the transcriptome analysis identified that there were 304, 1376 and 2083 differentially expressed genes (DEGs) in LSD vs MSD, MSD vs HSD and LSD vs HSD, respectively. Among them, most of the immune-related DEGs were down-regulated and metabolism-related DEGs were up-regulated with the increasing stocking density. In addition, KEGG enrichment pathway analysis revealed that several immune and metabolic related pathways including PI3K-Akt signaling pathway and AMPK signaling pathway were significantly enriched. Of these, the PI3K-Akt signaling pathway had the most DEGs and was also the most significantly enriched pathway. Furthermore, 16 DEGs (such as FOXO, PCK2 and CTSC, etc.) and partial immune enzyme activity (such as AST, CAT and PO, etc.) changes were closely correlated with the increase of stocking density when partial immune-related DEGs and immune-related enzymes were analyzed jointly. All these results indicated that changes in stocking density had a significant effect on the growth performance, immunity and transcriptome of L. vannamei.

Post-prandial response in hepatopancreas and haemolymph of Penaeus monodon fed different diets. Omics insights into glycoconjugate metabolism, energy utilisation, chitin biosynthesis, immune function, and autophagy

Raw materials or bioactive ingredients trigger mechanisms to assimilate nutrients and activate metabolic pathways that promote growth, immune function, or energy storage. Our understanding of these processes at a molecular level remains limited in aquaculture, especially in shrimp. Here, hepatopancreas proteomics and haemolymph metabolomics were used to investigate the post-prandial response of black tiger shrimps (Penaeus monodon) fed a conventional fishmeal diet (FM); a diet supplemented with the microbial biomass Novacq™ (NV); krill meal (KM); or, fasted (FS). Using FM as a control, a 2-fold change in abundance threshold was implemented to determine the significance of proteins and metabolites. NV fed shrimp showed preference for energy derived from carbohydrates indicated by a strong signature of glycoconjugate metabolism and activation of the amino- and nucleotide sugar metabolic pathway. KM activated the glyoxylate and dicarboxylate pathway that denoted shrimp preference for lipidic energy. KM also influenced energy generation by the TCA cycle inferred from higher abundance of the metabolites succinic semialdehyde, citric acid, isocitrate, alpha ketoglutarate and ATP and downregulation of the enzyme isocitrate dehydrogenase that catalyses oxidative decarboxylation of isocitrate. FS shrimp displayed down-regulation of oxidative phosphorylation and resorted to internal lipid reserves for energy homeostasis displaying a strong signature of autophagy. Pyrimidine metabolism was the preferred energy strategy in this group. Our study also provided evidence that during fasting or consumption of specific ingredients, shrimp share common pathways to meet their energy requirements, however, the intensity at which these pathways were impacted was diet dependent.

scRNA-seq analysis reveals toxicity mechanisms in shrimp hemocytes subjected to nitrite stress

In shrimp, hemocytes play an important role in detoxification and immune defense, and are where nitrite accumulates during exposure to this toxic environmental pollutant. However, the heterogeneity mechanisms of toxicity have not been reported under nitrite expose in shrimp. Here, we used single-cell RNA-seq to resolve 24,000 cells, which the responses of different cell populations of hemocytes under nitrite exposure in Penaeus vannamei. We identified 394 specific nitrite-responsive genes in 9 clusters of hemocytes, and found heterogeneity in the nitrite response of the three subpopulations of hemocytes (hyaline, semi-granular and granular cells). In hyaline, the response appeared modest, whereas nitrite-related dysregulation of metabolic processes in granular and semi-granular was pronounced. Ammonia nitrogen will rapidly accumulate in hemocytes of shrimp under nitrite stress. In semi-granular, excessive ammonia will interfere with oxidative phosphorylation and antioxidant system, thus inducing the production of reactive oxygen species. In granular, the abnormality of urea cycle caused by ammonia accumulation is the main toxic factor, which by inhibits arginase and arginine kinase. Collectively, our data provide a single-cell atlas for the dissection of shrimp hemocyte complexity, and reveal the toxicity mechanisms associated with nitrite exposure.

Effects of copper pyrithione (CuPT) on apoptosis, ROS production, and gene expression in hemocytes of white shrimp Litopenaeus vannamei

Copper pyrithione (CuPT) is used globally to prevent biofouling. However, it poses certain risks to aquatic ecosystems. To understand the effects of CuPT on Litopenaeus vannamei after exposure to different concentrations of CuPT (0, 64, and 128 μg/L), the apoptotic cell ratio, production of reactive oxygen species (ROS), and gene expression in the hemocytes were studied at 0, 3, 12, 24, and 48 h. The results revealed that ROS production was induced significantly at 3-48 h only in the 128 μg/L groups. The apoptotic cell ratio was increased significantly at 12 and 24 h in the 64 μg/L groups, and at 3-48 h in the 128 μg/L groups. Meanwhile, CuPT exposure changed gene expression in hemocytes at different levels. In the 64 μg/L groups, the expression of Mn-superoxide dismutase (MnSOD) was induced at 12 h, glutathione peroxidase (GPx) was induced at 24 and 48 h, caspase-3 induced at 24 h, metallothionein (MT) and HSP70 were increased at 3 h. In the 128 μg/L groups, MnSOD was increased at 3 h and then decreased at 12-48 h, GPx was up-regulated at 3, 24 h and then decreased at 48 h, caspase-3 was increased at 24 h, MT was increased at 3-48 h, HSP60 and HSP70 were up-regulated at 3-12 h. These results indicated that CuPT induced ROS production and the expression of caspase-3 in hemocytes, then caused hemocyte apoptosis. Expression levels of MnSOD, GPx, MT, HSP60, and HSP70 were up-regulated to protect the hemocyte against CuPT stress.

Transcriptomic analysis of Neocaridina denticulate sinensis hepatopancreas indicates immune changes after copper exposure

Neocaridina denticulate sinensis is a promising crustacean model species due to its merits in raising and breeding. However, its molecular responses to copper remains largely unknown. In the present research, RNA-seq was used to mine the alteration in transcriptome of N. denticulate sinensis hepatopancreas under copper exposure. A total of 16,423 DEGs was identified between control and Cu²⁺ treatment groups. GO enrichment analysis of all DEGs suggested down-regulated genes exceeded up-regulated genes in all the significantly enriched terms, except for RNA polymerase III complex (GO:0005666). KEGG analysis showed Cu exposure only induced two significantly enriched pathways, including Phagosome (ko04145) and Pathogenic Escherichia coli infection (ko05130). Besides, pattern recognition receptors as Toll, lectin B, CTL1 and SRB, AMPs as crustin type I, lysozyme, and NOS were down-regulated after Cu²⁺ exposure, while hemocyanin, MT, HSP70 and HSP90 were significantly up-regulated, implying these molecules may play vital role in Cu²⁺ detoxification of N. denticulate sinensis. Our results here provide research direction of heavy metal detoxification of N. denticulate sinensis, simultaneously enriched its genomic information.

Nitrite Stress Induces Oxidative Stress and Leads to Muscle Quality Decreased in Wuchang Bream (Megalobrama amblycephala Yih) Juveniles

To determine the effects of nitrite exposure on muscle quality and physiological functions in Wuchang bream (Megalobrama amblycephala), we exposed M. amblycephala juveniles to acute nitrite (0, 1, 5, 10, 20 mg/L), and the muscle and blood samples were measured at 12, 24, 48, and 96 h. The results showed that when exposed to nitrite for 12 h, the concentrations of blood glucose, cortisol, aspartate aminotransferase (AST), and alanine aminotransferase (ALT) in the 20 mg/L experimental group had the maximum value. The activity of lactate dehydrogenase (LDH) increased significantly in a dose-dependently manner and peaked at 96 h in the 20 mg/L group. During 96 h of exposure to nitrite, the total antioxidant capacity (T-AOC) and catalase (CAT) activity in the liver of the 20 mg/L experimental group were significantly higher than those of the control group, while the concentration of muscle glycogen showed a downtrend. At 12 h and 96 h, the hardness of the four experimental groups were significantly higher than that of the control group. Our research shows that acute sodium nitrite exposure will not only cause oxidative stress and decreased muscle quality in M. amblycephala juveniles but also will be accompanied by changes in serum biochemical index, liver antioxidant capacity, muscle physiological characteristics, and muscle physical characteristics. Preliminary speculation may be that acute nitrite exposure may cause M. amblycephala juveniles to choose to reduce muscle quality and activate antioxidant systems.

Tropical Cellulolytic Bacteria: Potential Utilization of Sugarcane Bagasse as Low-Cost Carbon Source in Aquaculture

Sugarcane bagasse (SB), as a major by-product of sugarcane, is one of the most abundant organic matter and characterized by cheap and easily available carbon source in Hainan Island, China. The objective of this study was to isolate tropical cellulolytic bacteria from Hainan Island and demonstrate their prospects of utilization of SB as a low-cost carbon source to greatly reduce the cost of aquaculture. A total of 97 cellulolytic marine bacteria were isolated, of which, 58 cellulolytic marine bacteria displayed the hydrolysis capacity (HC) of more than 1, while 28 cellulolytic marine bacteria displayed more than 2. Of the 28 tropical cellulolytic bacterial strains with HC more than 2, Microbulbifer sp. CFW-C18 and Vibrio sp. MW-M19 exhibited excellent SB decomposition in a small-scale laboratory simulation of shrimp aquaculture, up to 75.31 and 74.35%, respectively, and both of them were safe for shrimps. Meanwhile, both of CFW-C18 and MW-M19 besides displaying low multiple antibiotic resistance (MAR) index, also increased the C/N ratio (CFW-C18: C/N ratio of 14.34; MW-M19: C/N ratio of 14.75) of the small-scale laboratory simulation of shrimp aquaculture by decreasing the nitrogen content after a supplement of SB for 15 days. More importantly, CFW-C18 and MW-M19 displayed a relatively low MAR index, 0.47 and 0.1, respectively, especially MW-M19, with the lowest MAR index (0.1), which was resistant to only three antibiotics, streptomycin, amikacin, and levofloxacin, indicating that this strain was safe and non-drug resistance for further use. Overall, tropical cellulolytic bacteria isolated from Hainan Island, especially CFW-C18 and MW-M19, will provide the proficient candidates as probiotics for further construction of the recirculating aquaculture system based on the supplement of low-cost external carbon source—SB.

Multi-Strain Tropical Bacillus spp. as a Potential Probiotic Biocontrol Agent for Large-Scale Enhancement of Mariculture Water Quality

Aquaculture is suffering from long-term water eutrophication in intensive models, whereas the knowledge of multi-strain/specie for improving water quality is extremely limited. Herein, we aimed to develop multi-strain tropical Bacillus spp. as a potential probiotic biocontrol agent for large-scale enhancement of mariculture water quality. Given the practical application, the optimum multi-strain tropical Bacillus spp. (B. flexus QG-3, B. flexus NS-4, and B. licheniformis XCG-6 with the proportion 5: 5: 4) as a probiotic biocontrol agent was screened and obtained, which effectively improved water quality by removing chemical oxygen demand (COD), ammonia-nitrogen, and nitrate and significantly inhibited Vibrio spp. even at relatively low bacterial concentrations (10⁴ CFU/ml) in artificial feed wastewater and large-scale shrimp aquaculture ponds. More importantly, we found that the initial proportion of these three Bacillus sp. strains of multi-strain tropical Bacillus spp. markedly affected the final purification effects, whereas the initial concentration of that only influenced the purification rates at the early stage (0–48 h) instead of final purification effects. We reason that this multi-strain tropical Bacillus spp. as a good probiotic biocontrol agent could perform multiple actions, such as COD-degrading, nitrifying, denitrifying, and antagonistic actions, for large-scale enhancement of tropical aquaculture water. Additionally, the multi-strain tropical Bacillus spp. was safe for shrimp and could be stored for at least 240 days in spore form at room temperature. This multi-strain probiotic biocontrol agent may facilitate its adoption for further marine recirculating aquaculture system development and large-scale commercial application.

Community Structure of Protease-Producing Bacteria Cultivated From Aquaculture Systems: Potential Impact of a Tropical Environment

Protease-producing bacteria play vital roles in degrading organic matter of aquaculture system, while the knowledge of diversity and bacterial community structure of protease-producing bacteria is limited in this system, especially in the tropical region. Herein, 1,179 cultivable protease-producing bacterial strains that belonged to Actinobacteria, Firmicutes, and Proteobacteria were isolated from tropical aquaculture systems, of which the most abundant genus was Bacillus, followed by Vibrio. The diversity and relative abundance of protease-producing bacteria in sediment were generally higher than those in water. Twenty-one genera from sediment and 16 genera from water were identified, of which Bacillus dominated by Bacillus hwajinpoensis in both and Vibrio dominated by Vibrio owensii in water were the dominant genera. The unique genera in sediment or water accounted for tiny percentage may play important roles in the stability of community structure. Eighty V. owensii isolates were clustered into four clusters (ET-1-ET-4) at 58% of similarity by ERIC-PCR (enterobacterial repetitive intergenic consensus-polymerase chain reaction), which was identified as a novel branch of V. owensii. Additionally, V. owensii strains belonged to ET-3 and ET-4 were detected in most aquaculture ponds without outbreak of epidemics, indicating that these protease-producing bacteria may be used as potential beneficial bacteria for wastewater purification. Environmental variables played important roles in shaping protease-producing bacterial diversity and community structure in aquaculture systems. In sediment, dissolved oxygen (DO), chemical oxygen demand (COD), and salinity as the main factors positively affected the distributions of dominant genus (Vibrio) and unique genera (Planococcus and Psychrobacter), whereas temperature negatively affected that of Bacillus (except B. hwajinpoensis). In water, Alteromonas as unique genus and Photobacterium were negatively affected by NO₃ ^--N and NO₂ ^--N, respectively, whereas pH as the main factor positively affected the distribution of Photobacterium. These findings will lay a foundation for the development of protease-producing bacterial agents for wastewater purification and the construction of an environment-friendly tropical aquaculture model.

Exposure to benzo[a]pyrene triggers distinct patterns of microRNA transcriptional profiles in aquatic firefly Aquatica wuhana (Coleoptera: Lampyridae)

Larval aquatic fireflies in fresh water are adversely affected by water pollutants such as benzo(a)pyrene (BaP). However, their response to BaP stress at the microRNA (miRNA)-regulatory level remains unknown. Here, transcriptomes containing 31,872 genes and six miRNA transcriptional profiles were obtained for Aquatica wuhana larvae, and comparative analysis was performed between larvae exposed to BaP (0.01 mg/L) and unexposed controls. Fifteen of 114 miRNAs identified via bioinformatics were detected as differentially expressed (DEMs) upon BaP exposure. Analysis results of predicted target genes of DEM suggests that BaP exposure primarily triggered transcriptional changes of miRNA associated with five major regulatory categories: 1) osmotic balance, 2) energy metabolic efficiency, 3) development, 4) xenobiotic metabolism (oxidative stress), and 5) innate immune response. Based on six innate immune- and xenobiotic metabolism-related pathways enriched by the predicted DEM targets, 11 key BaP-responsive DEMs were further screened to investigate dynamic changes of expression in response to BaP stress at five time points, and also to validate the miRNA sequencing data using quantitative real-time PCR. This study provides valuable information for the protection of firefly resources and supplements the understanding of miRNA regulatory mechanisms in response to water deterioration.

Expression analysis of immune-associated genes in hemocytes of mud crab Scylla paramamosain under low salinity challenge

To gain knowledge on the immune response in Scylla paramamosain under low salinity challenge, S. paramamosain we investigated digital gene expression (DEG) in S. paramamosain hemocytes using the deep-sequencing platform Illumina Hiseq XTen. A total of 97,257 high quality unigenes with mean length 786.59 bp were found to be regulated by low salinity challenge, among which 93 unigenes were significantly up regulated, and 71 were significantly down regulated. Functional categorization and pathways analysis of differentially expressed genes revealed that immune signaling pathway including cAMP and cGMP signaling pathway were affected in low salinity stress. Cellular immunity-related genes including low-density lipoprotein receptor-related protein 6 (LRP6) and xanthine dehydrogenase (XDH) were down-regulated, indicating phagocytosis and oxygen dependent mechanism of phagocyte were suppressed in low salinity stress; Humoral immunity-related genes serine proteases and serpins 3 were up- and down-regulated, respectively, suggest that the proPO system was influenced by low salinity significantly; Moreover, processes related to immune response including carbohydrate metabolism, protein synthesis and lipid transport were found differentially regulated, implying the integrity of the immune response in low salinity stress. This study gained comprehensive insights on the immune mechanism of S. paramamosain at low salinity stress at the molecular level. The findings provide a theoretical basis for understanding immune mechanisms of S. paramamosain under low salinity stress, and technical reference for evaluating physiological adaptation in fresh water environment.

Construction of a High-Density Genetic Map and Identification of Quantitative Trait Loci for Nitrite Tolerance in the Pacific White Shrimp (Litopenaeus vannamei)

Nitrite is a major environmental toxin in aquaculture systems that disrupts multiple physiological functions in aquatic animals. Although nitrite tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available. In this study, we constructed a high-density genetic map of Litopenaeus vannamei with 17,242 single nucleotide polymorphism markers spanning 6,828.06 centimorgans (cM), with an average distance of 0.4 cM between adjacent markers on 44 linkage groups (LGs). Using this genetic map, we identified two markers associated with nitrite tolerance. We then sequenced the transcriptomes of the most nitrite-tolerant and nitrite-sensitive individuals from each of four genetically distinct L. vannamei families (LV-I–4). We found 2,002, 1,983, 1,954, and 1,867 differentially expressed genes in families LV-1, LV-2, LV-3, and LV-4, respectively. By integrating QTL and transcriptomics analyses, we identified a candidate gene associated with nitrite tolerance. This gene was annotated as solute carrier family 26 member 6 (SLC26A6). RNA interference (RNAi) analysis demonstrated that SLC26A6 was critical for nitrite tolerance in L. vannamei. The present study increases our understanding of the molecular mechanisms underlying nitrite tolerance in shrimp and provides a basis for molecular-marker-assisted shrimp breeding.

The impact of mercury on the genome-wide transcription profile of zebrafish intestine

Mercury is a widely used heavy metal that causes pollution to aquatic environments and severely affects the health of fish. Little is known about how heavy metal pollutants affect fish, particularly for gene expression within important organs such as the intestine. Herein, whole transcriptome sequencing was performed on zebrafish (Danio rerio) intestine tissue after HgCl₂ (HGC, 30 μg/L) exposure. A total of 2,257 differentially expressed genes (DEGs) were identified, including 1,788 up- and 469 down-regulated genes. Functional enrichment analysis revealed that these DEGs were primarily related to xenobiotic biodegradation, biomacromolecule metabolism, development, oxidative defense, and immune response. Ten key HGC-responsive DEGs were screened to survey the dynamic changes of expression in response to HGC exposure at different time points, and were also used to validate RNA sequencing data using quantitative real-time PCR (qPCR). Results indicate that the expression of genes encoding UGT1AB, GSTT1B, GSTO1, GSTM2, UGT5G1, GSTT1A, GSTR, GSTM3, GSTA1, and GSTP2 were significantly upregulated in response to the HGC exposure, and potentially help to counteract the adverse effects of HGC. This study provides insight into fish molecular toxicological responses to heavy metals and method on environmental risk assessment.

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.

Digital gene expression analysis in the gills of Ruditapes philippinarum after nitrite exposure

Due to the overload of pollutants from highly intensive anthropic activities, nitrite accumulates in offshore seawater and has been a long-lasting pollutant to the healthy aquaculture of the mollusk. In the present study, Ruditapes philippinarum was used as the target bivalve to receive nitrite exposure at environmental concentration for 1 and 7 days. Differentially expressed genes (DEGs) were detected and analyzed by a digital gene expression (DGE) approach to describe the toxicity of nitrite on the bivalve at the gene level. In the N1 group, 185 DEGs were generated and enriched in six Gene Ontology (GO) terms, including oxidoreductase activity, heme binding, tetrapyrrole binding, iron ion binding, metal binding and cation binding. The DEGs in the N1 group were also enriched in two Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, e.g., arachidonic acid metabolism and ovarian steroidogenesis. In the N7 group, 81 DEGs were generated without any GO enrichment but were enriched in five KEGG pathways, including protein processing in the endoplasmic reticulum, protein export, prion diseases, thyroid hormone synthesis and arachidonic acid metabolism. This suggested that nitrite exposure might cause adverse effects to the clams in several aspects, including oxidative damage, depressed immunity, and disorders in cell proliferation, hormone metabolism and tissue regeneration. Evaluation of oxidative stress indicated that nitrite exposure actually induced redox state imbalance by enhancing the contents of thiobarbituric acid reactive substances (TBARSs) and glutathione (GSH), and the activity of glutathione peroxidase (GSH-PX) but not superoxide dismutase (SOD). These results will provide valuable gene references for further study on the toxicology mechanism of bivalves under environmental nitrite stress.

Transcriptome analysis of hemocytes from the white shrimp Litopenaeus vannamei with the injection of dopamine

As a crucial neuroendocrine-immune factor, dopamine (DA) could regulate the immune system of Litopenaeus vannamei. To understand the immune mechanisms and regulatory pathways of DA in L. vannamei, the transcriptome analysis of hemocytes of L. vannamei with injection of DA (10^-6 mol/shrimp) at 3 and 12 h were performed in this study. Moreover, quantitative real-time PCR (qPCR) method was applied to validate the accuracy of transcriptome sequencing and analyze the expression pattern of candidate differentially expressed genes (DEGs) at different time points (0, 3, 6, 12, and 24 h) after DA injection. The results showed that a total of 51382 unigenes with a N50 length of 2341 bp were generated. And 1397 and 457 DEGs were obtained by comparative transcriptome at 3 and 12h respectively. Moreover, the results of functional annotation and enriched pathway showed that the DEGs were involved in phagosome (ko04145), lysosome (ko04142), Endocytosis (ko04144), and NOD-like receptor signaling pathway (ko04621). Besides, the Pearson's correlation coefficient (R) between transcriptome sequencing and qPCR was 0.845, which confirmed the reliability of the transcriptome sequencing results and the accuracy of assembly. Furthermore, the expression pattern of 15 candidate DEGs, containing 9 up-regulated and 6 down-regulated DEGs at 3 h, indicated the regulation of DA in physiological functions especially in the immune system. Therefore, these results revealed that DA induced the expressions of membrane receptors or proteins, activated intracellular signaling pathways, regulated cellular and humoral immune systems, controlled antioxidation and apoptosis, and was involved in the regulation of neuroendocrine system. These findings are helpful to promote the understanding on the effects of biogenic amines on physiological functions and regulatory networks of crustacean, and offer a substantial material and foundation for researching the immune response of crustacean.

Identification and functional characterization of a C-type lectin gene from Litopenaeus vannamei that is associated with ER-stress response

C-type lectins (CTLs), which bind carbohydrates in a Ca²⁺-dependent manner, are involved in many cellular activities, especially immunity. CTLs play important roles in both the antibacterial and the antiviral immune response and are also associated with autoimmunity. Several CTLs have been investigated in crustaceans, primarily with respect to their function in the immune response. In this study, we cloned a novel CTL gene (LvCTLU) from Litopenaeus vannamei. LvCTLU is involved in microbe agglutination and phagocytosis. Downregulating LvCTLU increased the cumulative mortality of L. vannamei after Vibrio parahemolyticus infection. Similar to other reported CTLs, LvCTLU also had antiviral properties. Downregulation of LvCTLU also increased the cumulative mortality of L. vannamei after infection with white spot syndrome virus. More importantly, LvCTLU expression was induced by the unfolded protein response (UPR), which is the key pathway in the endoplasmic reticulum (ER)-stress response of eukaryotic organism. Our results suggested that this protein might be involved in the shrimp ER-stress response. Reporter gene assay indicated that LvCTLU was regulated by X-box-binding protein 1, which is the key transcription factor in the UPR. Our study thus revealed that LvCTLU plays vital roles in both the anti-pathogen immune response and the ER-stress response.

Exposure time relevance of response to nitrite exposure: Insight from transcriptional responses of immune and antioxidant defense in the crayfish, Procambarus clarkii

To understand the toxic effects of nitrite exposure on crayfish, expression of genes involved in the immune system, the antioxidant defense, and the heat shock protein 70 (HSP70) was measured after 12, 24, and 48 h of different nitrite concentrations exposure in the hepatopancreas and hemocytes of Procambarus clarkii. Nitrite exposure up-regulated mRNA levels of cytoplasmic Mn superoxide dismutase (cMn-SOD), catalase (CAT), glutathione peroxidase (GPx), and glutathione-S-transferase (GST), after 24 h nitrite exposure. At 48 h, nitrite exposure decreased the mRNA levels of mitochondrial MnSOD (mMn-SOD), CAT, and GPx. High concentrations of nitrite at 48 h of exposure decreased expression of β-1,3-glucan-bingding protein in the hepatopancreas, and lysozyme expression in hemocytes. Nitrite exposure caused little effect on the heat shock protein 70 (HSP70) in hemocytes. Through overall clustering analysis, we found that 24 h of nitrite exposure caused stronger transcriptional responses. Our study indicated that the response of P. clarkii to acute nitrite exposure was exposure time-dependent. These results will help to understand the dynamic response pattern of crustaceans to nitrite pollution, and improve our understanding of the toxicological mechanisms of nitrite in crustaceans.

Transcriptome signatures of the Pacific white shrimp Litopenaeus vannamei hepatopancreas in response to stress in biofloc culture systems

Comparative transcriptome analysis via high throughput sequencing was applied to gain knowledge on the immune response in Litopenaeus vannamei reared in biofloc technology systems (BFT). Two types of carbon sources, namely, traditional carbon sources (molasses) and biodegradable polymers [hydroxybutyric acid-co-3-hydroxyvaleric acid (PHBV)] were used in BFT systems. Clear water systems without the addition of carbon sources were treated as the control. Water quality assays showed that the average concentrations of several stress factors, including nitrite, nitrate and TSS, were the highest in molasses-based BFT systems. After sequencing and comparing the transcriptome profiles of the L. vannamei hepatopancreas, 743 and 201 genes were significantly differentially expressed in molasses- and PHBV-based BFT systems, respectively. GO enrichment analysis, which was performed using the differentially expressed genes, revealed seven significantly over-represented GO terms in molasses-based BFT systems, including catabolic process, hydrolase activity, cellular localization, organic substance metabolic process, cellular metabolic process, establishment of localization and response to stress. The captured key genes were mainly involved in the pathways including cellular stress response, immune response and pathogen recognition. However, no GO terms were significantly over-represented in PHBV-based BFT systems compared with control. This study indicates that shrimp are subject to stress in BFT systems when molasses serves as the carbon source. Thus, PHBV may be a better alternative.

Transcriptomic responses of Caco-2 cells to Lactobacillus rhamnosus GG and Lactobacillus plantarum J26 against oxidative stress

Oxidative stress is the basic reason for aging and age-related diseases. In this study, we investigated the protective effect of 2 strains of lactic acid bacteria (LAB), Lactobacillus rhamnosus GG and L. plantarum J26, against oxidative stress in Caco-2 cells, and gave an overview of the mechanisms of lactic acid bacteria antioxidant activity using digital gene expression profiling. The 2 LAB strains provided significant protection against hydrogen peroxide (H₂O₂)-induced reduction in superoxide dismutase activity and increase in glutathione peroxidase activity in Caco-2 cells. However, inactive bacteria had little effect on alleviating oxidation stress in Caco-2 cells. Eight genes related to oxidative stress-FOSB, TNF, PPP1R15A, NUAK2, ATF3, TNFAIP3, EGR2, and FBN2-were significantly upregulated in H₂O₂-induced Caco-2 cells compared with untreated Caco-2 cells. After incubation of the H₂O₂-induced Caco-2 cells with L. rhamnosus GG and L. plantarum J26, 5 genes (TNF, EGR2, NUAK2, FBN2, and TNFAIP3) and 2 genes (NUAK2 and FBN2) were downregulated, respectively. In addition, the Kyoto Encyclopedia of Genes and Genomes indicated that some signaling pathways associated with inflammation, immune response, and apoptosis, such as Janus kinase/signal transducers and activators of transcription (Jak-STAT), mitogen-activated protein kinase (MAPK), nuclear factor-κB, and tumor necrosis factor, were all negatively modulated by the 2 strains, especially L. rhamnosus GG. In this paper, we reveal the mechanism of LAB in relieving oxidative stress and provide a theoretical basis for the rapid screening and evaluation of new LAB resources.

Transcriptomic analysis of gills provides insights into the molecular basis of molting in Chinese mitten crab (Eriocheir sinensis)

Chinese mitten crab (Eriocheir sinensis) is an economically important freshwater aquaculture species and is a model species for research on the mechanism of molting. This study aimed to identify important candidate genes associated with the molting process and to determine the role of gills in the regulation of molting with the help of transcriptomic analysis. The transcriptomes of crabs at different molting stages—postmolt (PoM), intermolt (InM), premolt (PrM) and ecdysis (E)—were de novo assembled to generate 246,232 unigenes with a mean length of 851 bp. A total of 86,634 unigenes (35.18% of the total unigenes) were annotated against reference databases. Significantly upregulated genes were identified in postmolt compared to intermolt (1,475), intermolt compared to premolt (65), premolt compared to ecdysis (1,352), and ecdysis compared to postmolt (153), and the corresponding numbers of downregulated genes were 1,276, 32, 1,573 and 171, respectively. Chitin synthase, endochitinase, chitinase A, chitinase 3, chitinase 6 and chitin deacetylase 1 were upregulated during the postmolt and ecdysis stages, while phosphoglucomutase 3 (PGM3), glucosamine 6-phosphate deaminase (GNPDA) and glucosamine glycoside hydrolase (nagZ) were upregulated during the intermolt and premolt stages compared to the other stages. The upregulated genes were enriched in several lipid-related metabolic pathways, such as “fatty acid elongation”, “glycerophospholipid metabolism” and “sulfur metabolism”. Meanwhile, three signaling pathways, including the “phosphatidylinositol signaling system”, the “calcium signaling pathway” and the “GnRH signaling pathway” were also enriched. Tetraspanin-18, an important effector gene in the lysosomal pathway involved in cell apoptosis, up-regulate with the beginning of molting (in premolt stage) and reach the top in the ecdysis stage, and barely expressed in the intermolt stage. The expression variations in the tetraspanin-18 gene indicated that it may play an important role in the beginning of molting cycle, which might be regulated by the stress of salinity. This study revealed that the gills could participate in chitin degradation, in reestablishment of the exoskeleton and the signaling process. Based on transcriptomic analysis of the gills, we not only explored novel molecular mechanisms of molting in E. sinensis but also acquired foundational genetic data for E. sinensis.

Comparative transcriptomic analysis provides insights into the response to the benzo(a)pyrene stress in aquatic firefly (Luciola leii)

Many studies have reported that behavior and bioluminescence of fireflies could be affected by changes in environment conditions. However, little is known about how the deterioration of the aquatic environment affects aquatic fireflies, particularly with respect to molecular responses following exposure to water pollutants, such as benzo(a)pyrene (BaP), which is a key indicator in environmental risk assessment because of the hazards it poses. Here, whole transcriptome sequencing and gene expression analysis were performed on freshwater fireflies (Luciola leii) exposed to BaP (concentration of 0.01 mg/L). Four transcriptomic libraries were constructed for the control and treatment groups, including two biological replicates. From the mixed pools (each pool contains 60 individuals from three time points), a total of 54,282 unigenes were assembled. Furthermore, 329,337 of Single-nucleotide Polymorphisms (SNPs) and 1324 of Simple Sequence Repeats (SSRs) were predicted using bioinformatics, which is useful for the future development of molecular markers. Subsequently, 2414 differently expressed genes (DEGs) were identified in response to BaP stress in comparison to the control, including 1350 up-regulated and 1064 down-regulated DEGs. Functional enrichment showed that these DEGs are primarily related to innate immunity; xenobiotic biodegradation and response, biomacromolecule metabolism, biosynthesis, and absorption. Eight key BaP-responsive DEGs were screened to survey the dynamic changes of expression in response to BaP stress at different time points, and to validate the RNA sequencing data using quantitative real-time PCR. The results indicate that the expression of genes encoding UGT, CYP3A, CYP9, CYP6AS5 and ADHP were induced, while those encoding UGT2B10L, PTGDS, and ALDH were reduced, to participate in response to the BaP exposure and potentially help counteract the adverse effects of BaP. This investigation provides insight into the toxicological response of fireflies to the occurrence of water deterioration.

Identification and characterization of differentially expressed genes in hepatopancreas of oriental river prawn Macrobrachium nipponense under nitrite stress

The oriental river prawn Macrobrachium nipponense is a highly adaptable, tolerant, and fecund freshwater prawn that inhabits a wide range of aquatic environments. The hepatopancreas of crustaceans is not only a site for secretion of digestive enzymes, and also plays important roles in several metabolic processes, such as lipid and carbohydrate metabolism. It is the main organ for the detoxification and immunity. In this study, high-throughput sequencing techniques were used to detect the effect of nitrite stress (10 mg/L nitrite-N for 48 h) on gene expression in the hepatopancreas of M. nipponense. A total of 13,769 million reads were harvested, and 94,534 transcripts were de novo assembled using Trinity software and produced 56,054 non-redundant transcripts. A total of 825 differentially expressed genes were obtained comparing 48 h nitrite stress with control group. In the analysis of GO and KEGG database, significant differences were found in 49 pathways. Immune-related pathways under nitrite stress included arginine and proline metabolism, glutamate metabolism, Jak-Stat signaling pathway, endocytosis, wnt signaling pathway, RIG-I-like receptor signaling pathway, TGF-beta signaling pathway, GnRH signaling pathway and phagosome. Apoptosis-related pathway was also significantly altered, such as lysosome and apoptosis. Remarkably, nitrite stress altered the expression patterns of key apoptosis genes (tetraspanins-like protein, LAMP, CD63, caspase 3C and Caspase 1) and immune genes (Serine proteinase-like protein, C-type lectin, daf-36, SOCS-2, alpha-2-macroglobulin), confirmed that nitrite-stress induce immune response and eventually even apoptosis. This study provided a new insight into the role of hepatopancreas in crustaceans, and further investigation will continue.

Genome-wide gene expression analysis reveals novel insights into the response to nitrite stress in gills of Branchiostoma belcheri

Amphioxus has been widely used as a model for the comparative immunology of vertebrates. Studies have reported that gene expression changes in the amphioxus gill in response to biotic stress, such as microbial and their mimic challenge, but little is known about how gene expression is affected by abiotic stress in the marine environment, such as nitrite. A lack of information regarding gene expression response to abiotic stress hinders a comprehensive understanding of gill defense response in amphioxus. Here, RNA sequencing was used to carry out gene expression profiling analyses of Branchiostoma belcheri gills under nitrite stress. Six libraries were created for the control and treatment groups, including three biological replicates. In total, 2416 differently expressed genes (DEGs) were detected in response to nitrite stress, of which 1522 DEGs were up-regulated in the treatment group in comparison to the control, while the remaining 894 DEGs were down-regulated genes. Functional enrichment revealed that these DEGs are primarily involved in disease, innate immunity, xenobiotic biodegradation and metabolism, and biomolecular processes and apoptosis. We screened 11 key nitrite-responsive DEGs to detect their expression responses to nitrite stress at different time points, and validate the sequencing data using real time quantitative PCR. The results indicated that the expression of gene encoding CYP3A, POD, CASPR1, GST, MAO, DDH, and XDH/XO were induced, while those encoding MRC, GT, DNASE1L, and RIPK5 were reduced, to participate in the anti-nitrite response. This study provides a useful resource for research of molecular toxicology in amphioxus under environmental stress.

Genome-wide transcriptional response of microRNAs to the benzo(a)pyrene stress in amphioxus Branchiostoma belcheri

Amphioxus, a cephalochordate found in sand habitats in shallow in-shore seawaters, has been widely used as a model in comparative immunology of chordates. However, the role of microRNAs (miRNAs) in amphioxus under abiotic stress, particularly xenobiotics with strong toxicity, remains largely unknown. Here, a widespread marine contaminant, benzo(a)pyrene (BaP) is used to evaluate its toxic effects on miRNA expression of amphioxus. Six small RNA libraries were sequenced from Branchiostoma belcheri. A total of 144 known and 157 novel miRNAs were identified using deep sequencing and bioinformatics approaches. A total of 58 differentially expressed miRNAs (DEMs) were screened, including 25 up- and 33 down-regulated DEMs under BaP stress. Target genes possibly regulated by DEMs were predicted, and their functional enrichment analyses were performed. Targets of DEMs are primarily involved in xenobiotic and cellular homeostasis, catabolic and transport process. They could be largely linked to nine immune- and toxin detoxification-related pathways, including metabolism of xenobiotics by cytochrome P450, drug metabolism-other enzymes, and drug metabolism-cytochrome P450, etc. Furthermore, quantitative real-time PCR (qRT-PCR) analysis for 12 key BaP-responsive DEMs validates the accuracy of deep sequencing. Experiments were then conducted to investigate their expression responses to BaP stress at different time intervals in detail to further determine their expression dynamic in responses of B. belcheri towards BaP exposure. This study, to the best of our knowledge, investigates the regulatory roles of miRNAs in the toxicological response of amphioxus for the first time, providing valuable information for the protection of lone existing cephalochordate amphioxus.

Fipronil-induced toxic effects in zebrafish (Danio rerio) larvae by using digital gene expression profiling

Fipronil residue has caused widespread concern around the world, especially after the recent "toxic eggs" event in seven European countries. To evaluate the effects of fipronil on vertebrates, zebrafish larvae were used as an animal model to examine the lethal effect, developmental phenotypes at high doses, and possible mechanisms of toxicity by employing digital gene expression (DGE) profiling at environmentally relevant doses. The results of acute toxicity test indicated that treatment with fipronil from 75 h post-fertilization (hpf) led to the death of larvae with a 96-h LC50 value of 459 μg/L, as well as abnormal development including bent spine and shortened body length. Besides, we obtained high-quality-sequencing DGE profilings at fipronil concentrations of 0.5, 5, and 50 μg/L, respectively. The results revealed that 44 differentially expressed genes, 10 GO terms, and 3 KEGG pathways were overlapped among the three concentrations. MIDN, one of the 44 differentially expressed genes, showed dose-dependent responses at the transcriptional level, indicating that it was possibly a potential biomarker to reflect fipronil toxicity in zebrafish. Furthermore, we presumed that the changing transcriptional level of AP-1 family was possibly a reason for bent spine and shortened body length in larvae exposed to fipronil. Concurrently, altered abundance of transcripts of the ELOVL family in a key step of fatty acid elongation could possibly lead to the accumulation of long-chain fatty acids. Collectively, our results suggested that exposure to fipronil caused lethal and developmental toxicity in zebrafish larvae, and demonstrated the need for a comprehensive understanding of the potential mechanisms of fipronil toxicity due to fipronil's frequent presence in the environment and its potential threat to human health.

Effects of waterborne nitrite on hematological parameters and stress indicators in olive flounders, Paralichthys olivaceus, raised in bio-floc and seawater

Juvenile olive flounders, Paralichthys olivaceus (mean weight 2.69 ± 0.31 g), were raised in bio-floc and seawater for six months, these P. olivaceus (mean weight 280.1 ± 10.5 g, mean length 28.37 ± 2.3 cm) were exposed to different concentrations of waterborne nitrite (0, 25, 50, 100, and 200 mg NO₂^-/L) for 7 days. None of the P. olivaceus individuals exposed to bio-floc and seawater containing waterborne nitrite concentrations of 200 mg/L for 7 days survived. Hematological parameters (hemoglobin and hematocrit) were significantly reduced by nitrite exposure. Regarding plasma components, the concentrations of glucose, glutamic oxalate transaminase (GOT), and glutamic pyruvate transaminase (GPT) increased significantly in response to nitrite exposure, whereas cholesterol concentrations significantly decreased. Stress indicators, including concentrations of plasma glucose, cortisol, and liver and gill concentrations of heat shock protein 70 (HSP70) were significantly increased by nitrite exposure. The results of the study indicate that nitrite exposure affected the hematological parameters and stress indicators of P. olivaceus raised in bio-floc and seawater, and these changes were more prominent in the P. olivaceus raised in seawater than those raised in bio-floc.

Transcriptome profiling of immune-responsive genes in the intestine of Cynoglossus semilaevis Günther challenged with Shewanella algae

To better understand gene expression in the intestine after Shewanella algae infection and provide insights into its immune roles in the tongue sole, Cynoglossus semilaevis, sequencing-based high-throughput RNA analysis (RNA-Seq) for the intestines between the control group and 12 h post-injection group was performed. After assembly, there was an average of 23,957,159 raw sequencing reads, and 23,943,491 clean reads were obtained after filtering out low-quality reads. Then, 383 differentially expressed genes (DEGs) in the intestines in response to S. algae infection were identified. Subsequently, gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the DEGs were conducted to further explore their functions. Among all of the pathways involved, sixteen pathways were related to the immune system, among which the complement and coagulation cascades pathway was the most prominent for immunity-related DEGs, followed by the leukocyte transendothelial migration pathway. Furthermore, the expression levels of twelve selected DEGs in the immune-related pathways were identified by quantitative real-time polymerase chain reaction, substantiating the reliability and reproducibility of the RNA-Seq results. In summary, this study represents an important genomic resource for understanding the potential immune role of the tongue sole intestine from the perspective of gene expression.

Black rockfish C-type lectin, SsCTL4: A pattern recognition receptor that promotes bactericidal activity and virus escape from host immune defense

C-type lectin (CTL) is an immune receptor and is received extensive attention of its important roles in immune response and immune escape. Some CTL, such as CTL4, has been well characterized in human and several other mammals, but much less documentation exists about the immunological function of CTL4 in lower vertebrates. In the present study, a C-type lectin domain family 4 member, SsCTL4, which is also high homology with CD209 antigen-like protein, from the teleost fish black rockfish (Sebastes schlegelii) was identified and examined at expression and functional levels. The open reading frame of SsCTL4 is 765 bp, and the deduced amino acid sequence of SsCTL4 shares 78%-84% overall identities with the C-type lectin of several fish species. In silico analysis identified several conserved C-type lectin features, including a carbohydrate-recognition domain and four disulfide bond-forming cysteine residues. Expression of SsCTL4 occurred in multiple tissues and was upregulated during bacterial and viral infection. Recombinant SsCTL4 (rSsCTL4) exhibited apparent binding activities against bacteria (Edwardsiella tarda and Vibrio anguillarum) and virus (infectious spleen and kidney necrosis virus, ISKNV). rSsCTL4 was able to agglutinate the Gram-negative and Gram-positive bacteria in a Ca²⁺-dependent manner. The agglutinating ability of rSsCTL4 was abolished in the absence of calcium or presence of mannose. rSsCTL4 also increased macrophage bactericidal activity. In the presence of rSsCTL4, fish exhibited enhanced resistance against bacterial infection but increased susceptibility to viral infections. Collectively, these results indicate that SsCTL4 serves as a pattern recognition receptor that not only promotes bactericidal activity, but may also serve as targets for virus manipulation of host defense system.

Transcriptome analysis of Pacific white shrimp (Litopenaeus vannamei) challenged by Vibrio parahaemolyticus reveals unique immune-related genes

Pacific white shrimp (Litopenaeus vannamei) is an important cultural species worldwide. However, Vibrio spp. infections have caused a great economic loss in Pacific white shrimp culture industry. The immune responses of Pacific white shrimp to the Vibrio spp. is not fully characterized. In this study, the transcriptomic profiles of L. vannamei hemocytes were explored by injecting with or without Vibrio parahaemolyticus. Totally, 42,632 high-quality unigenes were obtained from RNAseq data. Comparative genome analysis showed 2258 differentially expressed genes (DEGs) following the Vibrio challenge, including 1017 up-regulated and 1241 down-regulated genes. Eight DEGs were randomly selected for further validation by quantitative real-time RT-PCR (qRT-PCR) and the results showed that are consistent with the RNA-seq data. Due to the lack of predictable adaptive immunity, shrimps rely on an innate immune system to defend themselves against invading microbes by recognizing and clearing them through humoral and cellular immune responses. Here we focused our studies on the humoral immunity, five genes (SR, MNK, CTL3, GILT, and ALFP) were selected from the transcriptomic data, which were significantly up-regulated by V. parahaemolyticus infection. These genes were widely expressed in six different tissues and were up-regulated by both Gram negative bacteria (V. parahaemolyticus) and Gram positive bacteria (Staphylococcus aureus). To further extend our studies, we knock-down those five genes by dsRNA in L. vannamei and analyzed the functions of specific genes against V. parahaemolyticus and S. aureus by bacterial clearance analysis. We found that the ability of L. vannamei was significantly reduced in bacterial clearance when treated with those specific dsRNA. These results indicate that those five genes play essential roles in antibacterial immunity and have its specific functions against different types of pathogens. The obtained data will shed a new light on the immunity of L. vannamei and pave a new way for fighting against the bacterial infection in Pacific white shrimp.

Comparative transcriptomic analysis provides insights into antibacterial mechanisms of Branchiostoma belcheri under Vibrio parahaemolyticus infection

Amphioxus, a basal chordate, is widely considered to be an existing proxy of the invertebrate ancestor of vertebrates, and it exhibits susceptibility to various pathogen infections and pathogenic mimic challenges. Here, in order to understand more clearly its antibacterial mechanisms, we analyzed the ribosomal RNA (rRNA)-depleted transcriptome of Chinese amphioxus (Branchiostoma belcheri) infected with Vibrio parahaemolyticus (V. p.) via next-generation deep sequencing technology (RNA-seq). We identified a total of 3214 differentially expressed genes (DEGs) by comparing V. p.-infected and control transcriptome libraries, including 2219 significantly up-regulated and 995 significantly down-regulated DEGs in V. p.-infected amphioxus. The DEGs with the top 10 most dramatic expression fold changes after V. p. infection, as well as 53 immune-related DEGs (IRDs) belonging to four primary categories of innate immunity were analyzed further. Through gene ontology (GO) and pathway enrichment analysis, DEGs were found to be primarily related to immune processes, apoptosis, catabolic and metabolic processes, binding and enzyme activity, while pathways involving bacterial infection, immune signaling, immune response, cancer, and apoptosis were overrepresented. We validated the RNA-seq results by detecting the expression levels of 10 IRDs using qRT-PCR, and we surveyed the dynamic variation in gene expression for these IRDs at 0, 6, 12, 24, and 48 h after V. p.

TREATMENT

Subsequently, according to the RNA-seq results, the presence of a primitive Toll-like receptor (TLR)-mediated antibacterial immune signaling pathway was predicted in B. belcheri. This study provides valuable information regarding antibacterial immunity for further research into the evolution of immunity in vertebrates and broadens our understanding of the innate immune response against bacterial invasion in amphioxus.

Changes of Ammonia-Metabolizing Enzyme Activity and Gene Expression of Two Strains in Shrimp Litopenaeus vannamei Under Ammonia Stress

Ammonia stress can inhibit the survival and growth, and even cause mortality of shrimp. In this study, ammonia-metabolizing enzyme activities and gene expression were compared between two strains of L. vannamei under different ammonia-N (NH4+) concentrations (3.4, 13.8, and 24.6 mg/L). The results showed that elevated ammonia concentrations mainly increased glutamine synthetase (GSase) activities while inhibiting transglutaminase (TGase) activities in the muscle of both strains. Thus, we concluded that L. vannamei could accelerate the synthesis of glutamine from glutamate and NH4+ to alleviate ammonia stress. Compared with the muscle, the hepatopancreas plays a major role in ammonia stress and might be a target tissue to respond to the ammonia stress. Compared to the control group, the treatment of high ammonia concentrations reduced the hepatopancreas TGase (TG) gene expression and increased the gene expression rates of glutamate dehydrogenase-β (GDH-β) and GSase (GS) in both the muscle and the hepatopancreas of the two strains (p < 0.05). These genes (GDH-β and GS) in strain B were not only expressed earlier but also at levels higher than the expression range of strain A. At the gene level, strain B showed a more rapid and positive response than strain A. These data might help reveal the physiological responses mechanisms of shrimp adapt to ammonia stress and speed up the selective breeding process in L. vannamei.

Differential expression of microRNAs in hemocytes from white shrimp Litopenaeus vannamei under copper stress

MicroRNAs (miRNAs) are small noncoding RNAs that regulate diverse cellular processes, including organismal stress response, through posttranscriptional repression of gene transcripts. They are known to have antiviral functions in aquatic crustacean species, but little is known about the role of miRNAs against environmental stress caused by Cu, a common chemical contaminant in aquatic environment. We performed small RNA sequencing to characterize the differentially expressed microRNAs in Cu exposed shrimp. A total of 4524 known miRNAs and 73 novel miRNAs were significantly (P < .05) differentially expressed after Cu exposure. The peak size of miRNAs was 22 nt. Among them, 218 miRNAs were conserved across 115 species. The validation of 12 miRNAs by stem-loop quantitative RT-PCR were found to be coherent with the expression profile of deep sequencing data as evaluated with Pearson's correlation coefficient (r = 0.707). Target genes of these differentially expressed miRNAs related to immune defense, apoptosis, and xenobiotics metabolism also showed significant changes in expression under Cu stress. The present study provides the first characterization of L. vannamei miRNAs and some target genes expression in response to Cu stress, and the findings support the hypothesis that certain miRNAs along with their target genes might be essential in the intricate adaptive response regulation networks. Our current study will provide valuable information to take an insight into molecular mechanism of L. vannamei against environmental stress.

Exploring gene expression changes in the amphioxus gill after poly(I:C) challenge using digital expression profiling

Amphioxus, a cephalochordate, is a key model animal for studying the evolution of vertebrate immunity. Recently, studies have revealed that microRNA (miRNA) expression profiles change significantly in the amphioxus gill after immune stimulation, but it remains largely unknown how gene expression responds to immune stress. Elucidating gene expression changes in the amphioxus gill will provide a deeper understanding of the evolution of gill immunity in vertebrates. Here, we used high-throughput RNA sequencing technology (RNA-seq) to conduct tag-based digital gene expression profiling (DGE) analyses of the gills of control Branchiostoma belcheri and of those exposed to the viral mimic, poly(I:C) (pIC). Six libraries were created for the control and treatment groups including three biological replicates per group. A total of 1999 differently expressed genes (DEGs) were obtained, with 571 and 1428 DEGs showing up- or down-regulation, respectively, in the treatment group. Enrichment analysis of gene ontology (GO) terms and pathways revealed that the DEGs were primarily related to immune and defense response, apoptosis, human disease, cancer, protein metabolism, enzyme activity, and regulatory processes. In addition, eight DEGs were randomly selected to validate the RNA-seq data using real-time quantitative PCR (qRT-PCR), and the results confirmed the accuracy of the RNA-seq approach. Next, we screened eight key responding genes to examine the dynamic changes in expression levels at different time points in more detail. The results indicated that expressions of TRADD, MARCH, RNF31, NF-κb, CYP450, TNFRSF6B, IFI and LECT1 were induced to participate in the antiviral response against pIC. This study provides a valuable resource for understanding the role of the amphioxus gill in antiviral immunity and the evolution of gill immunity in vertebrates.

Genome-wide gene expression analysis in the amphioxus, Branchiostoma belcheri after poly (I: C) challenge using strand-specific RNA-seq

The gene expression associated with immune response to bacteria/bacterial mimic has been extensively analyzed in amphioxus, but remains largely unknown about how gene are involved in the immune response to viral invasion at expression level. Here, we analyze the rRNA-depleted transcriptomes of Branchiostoma belcheri using strand-specific RNA-seq in response to the viral mimic, poly (I:C) (pIC). A total of 5,317 differentially expressed genes were detected at treatment group by comparing with control. The gene with the most significant expression changes (top 15) after pIC challenge and 7 immune-related categories involving 58 differently expressed genes were scrutinized. By functional enrichment analysis of differently expressed genes, gene ontology terms involving response to stress and stimulus, apoptosis, catabolic and metabolic processes and enzyme activity were overrepresented, and several pathways related to immune signaling, immune response, cancer, apoptosis, viral disease, metabolism were activated after pIC injection. A positive correlation between the qRT-PCR and strand-specific RNA-seq data confirmed the accuracy of the RNA-seq results. Additionally, the expression of genes encoding NLRC5, CASP1, CASP6, CYP450, CAT, and MDA5 were induced in B. belcheri under pIC challenge. Our experiments provide insight into the immune response of amphioxus to pIC and valuable gene expression information for studying the evolution of antiviral immunity in vertebrates.

Genome-wide gene expression analysis of amphioxus (Branchiostoma belcheri) following lipopolysaccharide challenge using strand-specific RNA-seq

Amphioxus is the closest living proxy for exploring the evolutionary origin of the immune system in vertebrates. To understand the immune responses of amphioxus to lipopolysaccharide (LPS), 5 ribosomal RNA (rRNA)-depleted libraries of amphioxus were constructed, including one control (0 h) library and 4 treatment libraries at 6, 12, 24, and 48 h post-injection (hpi) with LPS. The transcriptome of Branchiostoma belcheri was analyzed using strand-specific RNA sequencing technology (RNA-seq). A total of 6161, 6665, 7969, and 6447 differentially expressed genes (DEGs) were detected at 6, 12, 24, and 48 hpi, respectively, compared with expression levels at 0 h. We identified amphioxus genes active during the acute-phase response to LPS at different time points after stimulation. Moreover, to better visualize the resolution phase of the immune process during immune response, we identified 6057 and 5235 DEGs at 48 hpi by comparing with 6 and 24 hpi, respectively. Through real-time quantitative PCR (qRT-PCR) analysis of 12 selected DEGs, we demonstrated the accuracy of the RNA-seq data in this study. Functional enrichment analysis of DEGs demonstrated that most terms were related to defense and immune responses, disease and infection, cell apoptosis, and metabolism and catalysis. Subsequently, we identified 1330, 485, 670, 911, and 1624 time-specific genes (TSGs) at 0, 6, 12, 24, and 48 hpi. Time-specific terms at each of 5 time points were primarily involved in development, immune signaling, signal transduction, DNA repair and stability, and metabolism and catalysis, respectively. As this is the first study to report the transcriptome of an organism with primitive immunity following LPS challenge at multiple time points, it provides gene expression information for further research into the evolution of immunity in vertebrates.

Long-term influence of cyanobacterial bloom on the immune system of Litopenaeus vannamei

Cyanobacteria are ubiquitously distributed in water on the Earth. It has long been known that the cyanobacterial bloom in aquaculture ponds can cause acute and massive deaths of shrimp. However, the long-term and chronic effects of the cyanobacterial bloom on shrimp are still poorly understood. In this study, the immune state of white pacific shrimp, Litopenaeus vannamei, surviving a naturally occurring cyanobacterial bloom was investigated and tracked for 70 d. Compared with the control, the growth of shrimp suffering high concentrations of cyanobacteria was obviously postponed. In these shrimp, the activities of the NF-κB, JAK/STAT and P38 MAPK immune signaling pathways and the expression of many antimicrobial peptide genes were down-regulated, whereas the expression of C-type lectins was significantly up-regulated. Although the mRNA level of lysozyme was reduced, the expression of the invertebrate-type lysozyme gene was increased. Furthermore, the concentration of hemocytes in hemolymph was greatly decreased, but the phagocytic activity of hemocytes was increased. These suggested that the cyanobacterial bloom has significant and complex influences on the immune system of shrimp, and in turn, alteration of the immune state could be a factor by which few shrimp can survive the cyanobacterial bloom. Thus, the current study could help further understand the interactions between the aquaculture water environment and the immune system of shrimp.