Ammonia Toxicity in the Bighead Carp (Aristichthys nobilis): Hematology, Antioxidation, Immunity, Inflammation and Stress

Ammonia is one of the main environmental pollutants that affect the survival and growth of fish. The toxic effects on blood biochemistry, oxidative stress, immunity, and stress response of bighead carp (Aristichthys nobilis) under ammonia exposure were studied. Bighead carp were exposed to total ammonia nitrogen (TAN) concentrations of 0 mg/L, 3.955 mg/L, 7.91 mg/L, 11.865 mg/L, and 15.82 mg/L for 96 h. The results showed that ammonia exposure significantly reduced hemoglobin, hematocrit, red blood cell, white blood cell count, and platelet count and significantly increased the plasma calcium level of carp. Serum total protein, albumin, glucose, aspartate aminotransferase, and alanine aminotransferase changed significantly after ammonia exposure. Ammonia exposure can induce intracellular reactive oxygen species (ROS), and the gene expression of antioxidant enzymes (Mn-SOD, CAT, and GPx) increases at the initial stage of ammonia exposure, while MDA accumulates and antioxidant enzyme activity decreases after ammonia stress. Ammonia poisoning changes the gene expression of inflammatory cytokines; promotes the gene expression of inflammatory cytokines TNF-α, IL-6, IL-12, and IL-1β; and inhibits IL-10. Furthermore, ammonia exposure led to increases in stress indexes such as cortisol, blood glucose, adrenaline, and T3, and increases in heat shock protein 70 and heat shock protein 90 content and gene expression. Ammonia exposure caused oxidative stress, immunosuppression, inflammation, and a stress reaction in bighead carp.

Influence of the Enzymatic Hydrolysis Using Flavourzyme Enzyme on Functional, Secondary Structure, and Antioxidant Characteristics of Protein Hydrolysates Produced from Bighead Carp (Hypophthalmichthys nobilis)

In the current study, bighead carp fish were used in conjunction with the flavourzyme enzyme to obtain (FPH) fish protein hydrolysates. The optimum conditions of the hydrolysis process included an enzyme/substrate ratio of 4% and a temperature of 50 °C and pH of 6.5. The hydrolysis time was studied and investigated at 1, 3, and 6 h, and the (DH) degree of hydrolysis was recorded at 16.56%, 22.23%, and 25.48%, respectively. The greatest yield value was 17.83% at DH 25.48%. By increasing the DH up to 25.48%, the crude protein and total amino acid composition of the hydrolysate were 88.19% and 86.03%, respectively. Moreover, more peptides with low molecular weight were formed during hydrolysis, which could enhance the functional properties of FPH, particularly the solubility property ranging from 85% to 97%. FTIR analysis revealed that enzymatic hydrolysis impacted the protein's secondary structure, as indicated by a remarkable wavelength of amide bands. Additionally, antioxidant activities were investigated and showed high activity of DDPH radical scavenging, and hydroxyl radical scavenging demonstrated remarkable activity. The current findings demonstrate that the functional, structural, and antioxidant characteristics of FPH might make it an excellent source of protein and suggest potential applications in the food industry.

Effects of Cathepsins on Gel Strength and Water-Holding Capacity of Myofibrillar Protein Gels from Bighead Carp (Aristichthys nobilis) under a Hydroxyl Radical-Generation Oxidizing System

This study investigates the effects of cathepsins on the gel strength and water-holding capacity (WHC) of myofibrillar protein gels from bighead carp (Aristichthys nobilis) under a hydroxyl radical-generation oxidizing system. The myofibrillar proteins were divided into control group (with cathepsins) and E64 group (without cathepsins). The changes of cathepsin B and cathepsin L activities, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), protein oxidation (total sulfhydryl and carbonyl contents), and chemical interactions (nonspecific association, ionic bonds, hydrogen bonds, hydrophobic interactions, and disulfides) of myofibrillar protein and gels, as well as the gel strength and WHC of two groups under 0–100 mM H₂O₂, were measured. The results indicated that mild oxidation (10 mM H₂O₂) made a better gel strength and WHC. Cathepsin B and L activities decreased with increasing H₂O₂ concentrations but their effects on myofibrillar protein degradation still existed during 0.1–50 mM H₂O₂, which was expressed by higher carbonyl contents and ionic bonds at 0.1 and 50 mM H₂O₂, higher total sulfhydryl contents at 0 mM H₂O₂, and a lower intensity of MHC and actin of the control group than the E64 group. Besides more protein degradation, cathepsin proteolysis also resulted in lower gel strength and WHC in control gels than E64 gels under mild oxidation, which could be explained by lower hydrophobic interaction and moderate disulfides bonds between gel protein molecules of control gels.

Comparison of different edible parts of bighead carp (Aristichthys nobilis) flavor

The study aims to obtain the information on taste and odor among different edible parts (white dorsal meat, white abdomen meat, white tail meat, and dark meat) of bighead carp. The results showed that the white dorsal meat and white abdomen meat had the higher content of total amino acids among all edible parts of bighead carp samples. The highest inosine monophosphate and adenosine monophosphate content presented in white abdomen meat, and the highest equivalent umami concentration value presented in dark meat. The principal component analysis result of electronic tongue and electronic nose showed significant differences in the overall taste and odor characteristics among four group samples. Additionally, 41, 30, 42, and 29 volatile compounds were identified by headspace solid-phase microextraction/gas chromatography-mass spectrometry among white dorsal meat, white abdomen meat, white tail meat, and dark meat of bighead carp, respectively. Based on the data of relative olfactory activity value (ROAV ≥ 1), 12 relative olfactory activity compounds may mainly contribute to the overall odor of bighead carp, including 2-methylbutanal, hexanal, heptanal, (E)-2-octenal, nonanal, dodecanal, undecanal, decanal, 3-methyl-1-pentanol, 1-octen-3-ol, (Z)-2-octen-1-ol, and eucalyptol. Furthermore, according to the Partial Least Squares Discriminant Analysis profile derived from the ROAV of 12 characteristic volatile compounds, significant variations in the odor of different edible parts of bighead carp. Overall, there was a significant difference in taste and odor among different edible parts of bighead carp, and this study may provide useful information for unraveling the flavor characteristics of each edible part of raw bighead carp. PRACTICAL APPLICATIONS: The comprehensive information on taste and odor among different edible parts (white dorsal meat, white abdomen meat, white tail meat, and dark meat) of bighead carp were obtained using liquid chromatography-mass spectrometry, automatic amino acid analyzer, electronic tongue (E-tongue), headspace solid-phase microextraction/gas chromatography-mass spectrometry (HS-SPME/GC-MS), and electronic nose (E-tongue), respectively. This study may provide useful information for unraveling the flavor characteristics of each edible part of raw bighead carp and improving the flavor of bighead carp products.

Updated Genome Assembly of Bighead Carp (Hypophthalmichthys nobilis) and Its Differences Between Male and Female on Genomic, Transcriptomic, and Methylation Level

Cyprinidae is one of the largest family in freshwater fishes, and it is most intensively cultured fish taxon of the world. However, studies about sex determination in this large family is still rear, and one of the reasons is lack of high quality and complete genome. Here, we used nanopore to sequence the genome of a male bighead carp, obtaining contig N50 = 24.25 Mb, which is one of the best assemblies in Cyprinidae. Five males and five females were re-sequenced, and a male-specific region on LG19 was confirmed. We find this region holds many male-specific markers in other Cyprinidae fishes, such as grass carp and silver carp. Transcriptome analyses of hypothalamus and pituitary tissues showed that several sex-specific differentially expressed genes were associated with steroid biosynthesis. The UCH64E gene, located in the male-specific region on LG19, showed higher expression levels in male than female tissues of bighead carp. The methyl-RAD of hypothalamus tissues between males and females indicated that the sexual methylation differences are significant in bighead carp. We also compared the methylation sites recognized using methyl-RAD and nanopore raw reads and found that approximately 73% of the methylation sites identified using methyl-RAD were within nanopore CpG sites.

Comparative analysis of the gut microbiota in bighead carp under different culture patterns

AIMS

To investigate the phylogenetic composition and functional potential of bighead carp (Hypophthalmichthys nobilis) gut microbiome in two rearing patterns (bighead carp polycultured with Oreochromis niloticus in pond A and bighead carp polycultured with Cyprinus carpio in pond B, respectively), as well as the changes of plankton in the cultured water at four different time points.

METHODS AND RESULTS

The intestinal contents were sequenced using Illumina HiSeq of bacterial 16S rRNA. Cyanophyta and Chlorophyta were the prevalent phytoplankton in the water, whereas Rotifers and Protozoa were the predominant zooplankton. In all, 779,563 quality-filtered sequences and 8870 amplicon sequence variants were obtained from 24 samples that numbered T1A1 to T4A3 and T1B1 to T4B3, resulting in 35 phyla, with Proteobacteria, Firmicutes, Fusobacteria and Cyanobacteria dominating. According to alpha diversity and beta diversity measurements, the bacterial communities were diverse, Chao1 richness and Pielou's evenness were significantly lower in the T2B and T4B groups. The gut bacterial communities of T1A, T1B, T2A and T2B groups differed from those of other samples, which formed distinctly clusters with principal coordinate analysis and non-metric multidimensional scaling analysis. PICRUSt2 predictive function analysis revealed that different culture patterns influenced the gut microbiota metabolic capacity.

CONCLUSIONS

Intestinal bacteria belonging to the phyla Proteobacteria, Firmicutes, Cyanobacteria and Fusobacteria are better suited to inhabit in various environments and perform specific functions. Furthermore, contact with the external environment and nutrient intake also stimulate the variety of intestinal microbiotas in polycultured bighead carp.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first comprehensive, high-throughput investigation of gut microbiota diversity in bighead carp during various seasons in two polycultured patterns and provide preliminary information on gut microbiome composition and changes, laying a crucial foundation for future research on fish culture patterns in various environments.

Identifying Candidate Genes Involved in the Regulation of Early Growth Using Full-Length Transcriptome and RNA-Seq Analyses of Frontal and Parietal Bones and Vertebral Bones in Bighead Carp (Hypophthalmichthys nobilis)

Growth, one of the most important traits monitored in domestic animals, is essentially associated with bone development. To date, no large-scale transcriptome studies investigating bone development in bighead carp have been reported. In this study, we applied Isoform-sequencing technology to uncover the entire transcriptomic landscape of the bighead carp (Hypophthalmichthys nobilis) in early growth stage, and obtained 63,873 non-redundant transcripts, 20,907 long non-coding RNAs, and 1,579 transcription factors. A total of 381 alternative splicing events were seen in the frontal and parietal bones with another 784 events simultaneously observed in the vertebral bones. Coupling this to RNA sequencing (RNA-seq) data, we identified 27 differentially expressed unigenes (DEGs) in the frontal and parietal bones and 45 DEGs in the vertebral bones in the fast-growing group of fish, when compared to the slow-growing group of fish. Finally, 15 key pathways and 20 key DEGs were identified and found to be involved in regulation of early growth such as energy metabolism, immune function, and cytoskeleton function and important cellular pathways such as the arginine and proline metabolic pathway (p4ha1), FoxO signaling pathway (sgk1), cell adhesion molecules (b2m, ptprc, and mhcII), and peroxisome proliferator-activated receptor signaling pathway (scd). We established a novel full-length transcriptome resource and combined it with RNA-seq to elucidate the mechanism of genetic regulation of differential growth in bighead carp. The key DEGs identified in this study could fuel further studies investigating associations between growth and bone development and serve as a source of potential candidate genes for marker-assisted breeding programs.

Whole genome sequencing of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) provide novel insights into their evolution and speciation

The edible silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis), which are two of the "Four Domesticated Fish" of China, are cultivated intensively worldwide. Here, we constructed 837- and 845-Mb draft genome assemblies for the silver carp and the bighead carp, respectively, including 24,571 and 24,229 annotated protein-coding genes. Genetic maps, anchoring 71.7% and 83.8% of all scaffolds, were obtained for the silver and bighead carp, respectively. Phylogenetic analysis showed that the bighead carp formed a clade with the silver carp, with an estimated divergence time of 3.6 million years ago; the time of divergence between the silver carp and zebrafish was 50.7 million years ago. An East Asian cyprinid genome-specific chromosome fusion took place ~9.2 million years after this clade diverged from the clade containing the common carp and Sinocyclocheilus. KEGG and GO analyses indicated that the expanded gene families in the silver and bighead carp were associated with diseases, the immune system and environmental adaptations. Genomic regions differentiating the silver and bighead carp populations were detected based on the whole-genome sequences of 42 individuals. Genes associated with the divergent regions were associated with reproductive system development and the development of primary female sexual characteristics. Thus, our results provided a novel systematic genomic analysis of the East Asian cyprinids, as well as the evolution and speciation of the silver carp and bighead carp.

Cardiac Transcriptomics Reveals That MAPK Pathway Plays an Important Role in Hypoxia Tolerance in Bighead Carp (Hypophthalmichthys nobilis)

As aquatic animals, fishes often encounter various situations of low oxygen, and they have evolved the ability to respond to hypoxia stress. Studies of physiological and molecular responses to hypoxia stress are essential to clarify genetic mechanisms underlying hypoxia tolerance in fish. In this study, we performed acute hypoxia treatment in juvenile bighead carp (Hypophthalmicthys nobilis) by decreasing water O₂ from 6.5 mg/L to 0.5 mg/L in three hours. This hypoxia stress resulted in a significant increase in blood lactate and serum glucose. Comparisons of heart transcriptome among hypoxia tolerant (HT), hypoxia sensitive (HS), and normoxia control (NC) groups showed that 820, 273, and 301 differentially expressed genes (DEGs) were identified in HS vs. HT, NC vs. HS, and NC vs. HT (false discovery rate (FDR) < 0.01, Fold Change> 2), respectively. KEGG pathway enrichment showed that DEGs between HS and HT groups were mainly involved in mitogen-activated protein kinase (MAPK) signaling, insulin signaling, apoptosis, tight junction and adrenergic signaling in cardiomyocytes pathways, and DEGs in MAPK signaling pathway played a key role in cardiac tolerance to hypoxia. Combined with the results of our previous cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis of hypoxia stress in this species, such genes as stbp2, ttn, mapk, kcnh, and tnfrsf were identified in both studies, representing the significance of these DEGs in hypoxia tolerance in bighead carp. These results provide insights into the understanding of genetic modulations for fish heart coping with hypoxia stress and generate basic resources for future breeding studies of hypoxia resistance in bighead carp.

Immunohistochemical distribution of glucagon-like peptide 1 in the digestive system of different aquatic vertebrates

The distribution of glucagon-like peptide 1 (GLP-1)-positive cells in digestive tracts and pancreases of aquatic vertebrates was investigated by immunohistochemical staining method. The results suggested that GLP-1-positive cells were distributed in the columnar mucous epithelium and tubular glands of lamina propria in the digestive system. However, GLP-1-positive cells were also found in subepithelial lamina propria of the mucosae and muscularis in each segment of the digestive tract of Rana nigromaculata. The distribution densities of these cells reached peaks in the stomachs, and the middle or end segments of small intestines of Chinese softshell turtle, Bufo gargarizans, R. nigromaculata and catfish, and there was the third distribution density peak in the rectum of catfish. The total amount or overall density of GLP-1-positive cells varied a lot in the digestive tracts of different animal species. The distribution density was relatively low in the digestive tract of chub and reached the maximum in the digestive tracts of snakehead and catfish, but no GLP-1-positive cells were found in the digestive tract of bighead carp. GLP-1-positive cells were densely distributed in the pancreases of Chinese softshell turtle, B. gargarizans and R. nigromaculata. These cells spread over the superficial layers of islets or scattered in exocrine pancreas in the pancreas of B. gargarizans, spread in the endocrine cells or scattered in the pancreas of Chinese softshell turtle, scattered in the pancreas of R. nigromaculata and distributed in the superficial layers of islets in the pancreas of catfish.

Refinement of eDNA as an early monitoring tool at the landscape-level: study design considerations

Natural resource managers use data on the spatial range of species to guide management decisions. These data come from survey or monitoring efforts that use a wide variety of tools. Environmental DNA (eDNA) is a surveillance tool that uses genetic markers for detecting species and holds potential as a tool for large-scale monitoring programs. Two challenges of eDNA-based studies are uncertainties created by imperfect capture of eDNA in collection samples (e.g., water field samples) and imperfect detection of eDNA using molecular methods (e.g., quantitative PCR). Occurrence models can be used to address these challenges, thus we use an occurrence model to address two objectives: first, to determine how many samples were required to detect species using eDNA; second, to examine when and where to take samples. We collected water samples from three different habitat types in the Upper Mississippi River when both Bighead Carp and Silver Carp were known to be present based on telemetry detections. Each habitat type (backwater, tributary, and impoundment) was sampled during April, May, and November. Detections of eDNA for both species varied across sites and months, but were generally low, 0-19.3% of samples were positive for eDNA. Overall, we found that eDNA-based sampling holds promise to be a powerful monitoring tool for resource managers; however, limitations of eDNA-based sampling include different biological and ecological characteristics of target species such as seasonal habitat usage patterns as well as aspects of different physical environments that impact the implementation of these methods such as water temperature.

Body condition (Wr ) and reproductive potential of bighead and silver carp hybrids: Postzygotic selection in the Mississippi River Basin

Invasive bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are reproductively isolated in their native range, but form a bimodal, multigenerational hybrid swarm within the Mississippi River Basin (MRB). Despite observed F1 hybrid superiority in experimental settings, effects of postzygotic selection on bighead and silver carp hybrids have not been tested in a natural system. Individual parent and hybrid genotypes were resolved at 57 species-specific loci and used to evaluate postzygotic selection for body condition (Wr ) and female reproductive potential (presence of spawning stage gonads and gonadosomatic index [GSI]) in the MRB during 2009-2011. Body condition in the Marseilles Reach, Illinois River declined with a decrease in species-specific allele frequency from 1.0 to 0.4 for each species and early generation hybrids (F1, F2, and first-generation backcross) had lower mean Wr than late generation hybrids (2nd+ generation backcrosses) and parentals. Proportions of stage IV and stage V (spawning stage) female gonads differed between bighead and silver carp, but not among parentals and their early and late generation hybrids within the MRB. Mean GSI values did not differ between parentals and hybrids. Because reproductive potential did not differ between hybrids and parentals, our results suggest that early generation hybrids occur in low frequency either as a factor of poor condition (Wr ) and postreproductive survival, infrequent reproductive encounters by parental bighead and silver carp, or selection pressures acting on juvenile or immature life stages. Our results suggest that a combination of genetic and environmental factors may contribute to the postzygotic success of bighead and silver carp hybrids in the Mississippi River Basin.

Effect of sodium alginate coating enriched with horsemint (Mentha longifolia) essential oil on the quality of bighead carp fillets during storage at 4°C

Effect of sodium alginate coating enriched with horsemint essential oil (HEO) on the quality of bighead carp (Aristichthys nobilis) fillets at refrigeration temperature (4 ± 1°C) was studied. Bighead carp fillets were coated with neat sodium alginate (SA) and sodium alginate containing 0.5 and 1% v/v of HEO and their quality changes in terms of total volatile basic nitrogen (TVB-N), peroxide value (PV), thiobarbituric acid (TBA), and microbial counts were investigated. SA coating enriched with the essential oil could reduce the spoilage of the fillets and extend their shelf-life. Samples treated with SA-containing HEO showed significantly (P < 0.05) lower TVB-N content and lipid oxidation, as reflected by lower PV, FFA and TBA values during the storage period compared with the SA and control. The treatment also reduced the degree of microbial deterioration of the fillets (about 1.5 log10 CFU/g) more efficiently than the SA.

Confocal microscopy as a useful approach to describe gill rakers of Asian species of carp and native filter-feeding fishes of the upper Mississippi River system

To better understand potential diet overlap among exotic Asian species of carp and native species of filter-feeding fishes of the upper Mississippi River system, microscopy was used to document morphological differences in the gill rakers. Analysing samples first with light microscopy and subsequently with confocal microscopy, the three-dimensional structure of gill rakers in Hypophthalmichthys molitrix, Hypophthalmichthys nobilis and Dorosoma cepedianum was more thoroughly described and illustrated than previous work with traditional microscopy techniques. The three-dimensional structure of gill rakers in Ictiobus cyprinellus was described and illustrated for the first time.

Practical success of biomanipulation using filter-feeding Fish to control cyanobacteria blooms: a synthesis of decades of research and application in a subtropical hypereutrophic lake

Lake Donghu is a 32-km2 shallow, subtropical lake near the Yangtze River (P.R. China) that has experienced dramatic changes in the past five decades. These changes include: (1) a trophic state change from mesotrophy to hypertrophy; (2) dense blooms of cyanobacteria during every summer from the 1970s to 1984; (3) a cessation of blooms starting in 1985, with no recurrence; and (4) an increase, coincident with bloom declines, in the production of silver and bighead carp (filter-feeders) by more than tenfold. There are several possible explanations for the disappearance of blooms, including changes in nutrient concentrations, increased zooplankton grazing, and increased grazing on algae by fish. The long-term data suggest that changes in nutrients or in zooplankton were not important, but that the remarkably increased fish densities might have played the key role. To test this hypothesis, in situ enclosure experiments were conducted in three years. The main conclusions are as follows: (1) an increased stocking of the lake with carp played a decisive role in the elimination of cyanobacteria blooms; (2) both silver and bighead carp can eliminate cyanobacteria blooms directly by grazing; (3) zooplankton cannot suppress the blooms; and (4) the lake still is vulnerable to the outbreak of blooms, should fish grazing decline. The critical biomass of carp is approximately 50 g m3. The results suggest the applicability of a new food-web manipulation (increased stocking with filter-feeding fish) for controlling cyanobacteria blooms in hypereutrophic lakes. The approach differs from traditional biomanipulation in Europe and North America, where piscivores are added to control planktivores, and this in turn increases zooplankton and decreases algae. The new biomanipulation method is being used or being tested to counteract cyanobacteria blooms in many Chinese lakes such as Lake Dianchi in Yunnan Province, Lake Chaohu in Anhui Province, and Lake Taihu in Jiangsu Province. The method has great potential as an important component of an integrated approach to counteract cyanobacteria blooms, especially in lakes where nutrient inputs cannot be reduced sufficiently, and where zooplankton cannot effectively control phytoplankton production.