Long-Term Phellodendri Cortex Supplementation in the Tiger Grouper (Epinephelus fuscoguttatus): Dual Effects on Intestinal Health Revealed by Transcriptome Analysis

The tiger grouper (Epinephelus fuscoguttatus), an important mariculture fish in Southeast Asia, faces increasing health issues in recent years. Phellodendri Cortex (PC) is a traditional Chinese herbal medicine that exhibits a variety of beneficial effects on tiger groupers. The effects of PC, however, varies with the period of dietary intervention. This study aims to investigate the long-term effects of 1% PC supplementation on tiger groupers, focusing on growth, immunity, disease resistance, and intestinal gene expression. The tiger groupers (with an initial mean weight of 27.5 ± 0.5 g) were fed with a diet of Phellodendri Cortex supplementation and a control diet for 8 weeks. Our results indicate that the long-term PC supplementation did not affect growth or Vibrio disease resistance in tiger groupers. However, the transcriptome analysis revealed potential damage to the structural and functional integrity of the groupers' intestines. On the other hand, anti-inflammatory and cathepsin inhibition effects were also observed, offering potential benefits to fish enteritis prevention and therapy. Therefore, long-term PC supplementation in grouper culture should be applied with caution.

The effects of amino acids and fatty acids on the disease resistance of Epinephelus fuscoguttatus in response to Vibrio vulnificus infection

Mass mortality resulting from bacterial infection poses a major problem in the grouper aquaculture industry. The purpose of this study was to profile the metabolites released in challenged fish and to reconstruct the metabolic pathways of brown marble grouper (Epinephelus fuscoguttatus) in response to Vibrio vulnificus infection. Metabolite profiles from control and challenged treatment groups after feeding were determined using gas chromatography-mass spectrometry (GC-MS). Forty metabolites were identified from the GC-MS analysis. These metabolites comprised of amino acids, fatty acids, organic acids and carbohydrates. The profiles showed the highest percent area (33.1%) for leucine from the amino acid class in infected fish compared to the control treatment group (12.3%). Regarding the fatty acid class, a higher percent area of the metabolite 8,11-eicosadienoic acid (27.04%) was observed in fish infected with V. vulnificus than in the control treatment group (22.5%). Meanwhile, in the carbohydrate class, glucose (47.0%) was the metabolite in the carbohydrate class present at highest percentage in the control treatment group compared to infected fish (30.0%). Our findings highlight the importance of a metabolic analysis for understanding the changes of metabolites in E. fuscoguttatus in response to bacterial infections.

The complete mitochondrial genome of the hybrid grouper Epinephelus fuscoguttatus (♀) × E. polyphekadion (♂)

This study determined the complete mitochondrial genome of the hybrid grouper Epinephelus fuscoguttatus ♀ × E. polyphekadion ♂. The complete mitochondrial genome is 16,648 bp and includes 13 protein-coding, 2 ribosomal RNA, 22 transfer RNA genes, and a control region (D-loop). The nucleotide composition of the L-strand was A 29.12%, C 28.33%, G 15.65%, and T 26.90%. All except the NADH dehydrogenase subunit (ND6) and eight tRNA genes are encoded on the H-strand.

Hybridization of tiger grouper (Epinephelus fuscoguttatus ♀) x giant grouper (Epinephelus lanceolatus ♂) using cryopreserved sperm

Using Ringer solution as extender, the present study examined the protective effect of dimethyl sulphoxide (Me₂SO; 8-12%, v/v) on the cryopreservation of giant grouper (Epinephelus lanceolatus) sperm. The cryopreserved sperm was then successfully applied in interspecific hybridization with tiger grouper (E. fuscoguttatus). Higher motility (90.56 ± 6.58%) and fertilization rate (69.61 ± 4.83%) was achieved in 10% Me₂SO with Ringer solution as extender (dilution ratio 1:1), which should no significant difference in comparison with fresh sperm (95.88 ± 1.64% and 73.10 ± 1.28%). There were no statistical differences in both fertilization and hatching rates between hybrid and non-hybrid tiger grouper by using cryopreserved sperm for fertilization, but malformation rate of the hybrid was higher than non-hybrid (17%) (P < 0.05). Survival rate of the hybrid was lower than that of the controls at 15 days post hatching (23% vs 48%). However, hybrids showed survival rate equal to the controls at the end of the 60-day study period. Hybridization of E. fuscoguttatus x E. lanceolatus was successfully achieved using cryopreserved sperm from giant grouper. The cryopreservation of giant grouper sperm and its application in hybridization provided a technical support for further grouper breeding work.

Identification of Candidate Growth-Related SNPs and Genes Using GWAS in Brown-Marbled Grouper (Epinephelus fuscoguttatus)

Brown-marbled grouper, Epinephelus fuscoguttatus, is not only an important commercial fish species, but also an important crossbreeding parent in grouper industry. Improvement of growth traits of this species contributes to the development of grouper breeding. Currently, the development of molecular marker associated with growth of brown-marbled grouper is rare. Thus, we performed the first genome-wide association study (GWAS) for five growth traits in 172 brown-marbled groupers with 43,688 SNPs detected by ddRAD-seq. We identified a total of 5 significant and 18 suggestive QTLs located in multiple chromosomes associated with growth traits. In the 20 kb window of the significant SNPs and suggestive SNPs, 5 and 14 potential candidate genes affecting growth were detected, respectively. Five potential candidate genes near the significantly associated SNPs were selected for expression analysis. Among of which, bmp2k, wasf1, and acyp2 involved in bone development, maintenance of mitochondrion structure, and metabolism were differentially expressed. Interestingly, the SNP 23:29601315 located in the intron of bmp2k was significantly associated with body weight, body length, body height, and body thickness and suggestively associated with total length. We verified the locus using another new group including 123 individuals. The results showed that individuals with CC genotype have better growth traits comparing other individuals. Our findings not only contribute to understanding the molecular mechanism of growth regulation, but also promote the advance of marker-assisted selection in brown-marbled grouper.

Effects of Ascorbic Acid and β-1,3-Glucan on Survival, Physiological Response and Flesh Quality of Cultured Tiger Grouper (Epinephelus fuscoguttatus) during Simulated Transport in Water

Transport in water is the most common method for achieving high survival rates when transporting cultured fish in China; yet, transport success relies on proper water quality and conditions. This research was designed to explore the effects of ascorbic acid and β-1,3-glucan on survival, physiological responses, and flesh quality of farmed tiger grouper (Epinephelus fuscoguttatus) during simulated transport. The transport water temperature for live tiger grouper was 15 °C, which had the highest survival rate, the lowest stress response, and metabolic rate, and this will reduce the susceptibility to diseases. It is stated that β-1,3-glucan influences the changes of cortisol content, heat shock protein 70, IL-1β, and IgM transcription levels during simulated transport. Rather than using ascorbic acid alone (the A-group), β-1,3-glucan (3.2 mg/L) in the presence of ascorbic acid (25 mg/L) can effectively reduce the increase of transport-induced serum cortisol content, heat shock protein 70, and IL-1β, but stimulated IgM. 25 mg/L ascorbic acid and 3.2 mg/L β-1,3-glucan had no obvious effect on the nutritional indexes and flavor of live tiger grouper; however, these can effectively reduce the stress response, improve the innate immune activity, and ensure a higher survival rate.

Metabolite profiling of Epinephelus fuscoguttatus infected with vibriosis reveals Omega 9 as potential metabolite biomarker

In this study, we report the starvation effect and vibriosis infection on a tropical fish, the tiger grouper (Epinephelus fuscoguttatus). The tiger groupers were infected with Vibrio vulnificus for 21 days. Gas chromatography-mass spectrometry combined with multivariate analysis was used to assess the variation in metabolite profiles of E. fuscoguttatus. Metabolite productions in infected fishes were significantly influenced by fatty acid production. The Omega 9 (ω-9) was abundant under the challenged conditions compared to Omega 3 (ω-3) and Omega 6 (ω-6). A total of six fatty acids from the ω-9 group were detected in high concentration in the infected fishes compared to the control groupers. These metabolites are Oleic acid, Palmitoleic acid, 6,9-Octadecenoic acid, 8,11-Eicosadienoic acid, cis-Erucic acid and 5,8,11-Eicosatrienoic acid. The production of ω-9 differed significantly (p ≤ 0.001) in the challenged samples. The detected ω-9 compounds were quantified based on three different extraction techniques with Supelco 37-component FAME mix (Supelco, USA). The highest concentration of ω-9 groups compared to the other fatty acids detected is 1320.79 mg/4 g and the lowest is 939 mg/4 g in challenged-starved; meanwhile, in challenged-fed, the highest concentration detected is 1220.87 mg/4 g and the lowest is 917.25 mg/4 g. These changes demonstrate that ω-9 can be used as a biomarker of infection in fish.

Serum cortisol level and survival rate of juvenile Epinephelus fuscoguttatus following exposure to different salinities

Background and Aim:

Brown-marbled grouper Epinephelus fuscoguttatus is a premium marine food fish with high demand in Asia. In fish, stress due to environmental changes such as fluctuations in the salinity can result in increased cortisol level. Stress in fish increases susceptibility to diseases ultimately resulting in death. Therefore, the aim of this study was to investigate the salinity tolerance of E. fuscoguttatus and their survival in lower salinities.

Materials and Methods:

In this study, grouper juveniles (92.43±standard error of the mean 0.51 mm) maintained in 31 ppt seawater were transferred into five tanks with seawater diluted to 25, 20, 15, 10, and 5 ppt. The salinity of the control group was not changed and was maintained at 31 ppt. Serum cortisol was measured using ELISA at 0, 30, 60, and 120 min after the fish were transferred to the different concentrations of salinity.

Results:

The survival percentage was recorded for 14 days following the transfer and the results revealed that serum cortisol of fish in a high change in salinity (15, 10, and 5 ppt) was significantly higher than the control group immediately after exposure. At the high salinity change, the cortisol levels gradually decrease at 30 min and 60 min, until no difference in cortisol concentration was observed at 120 min. No mortality was observed in fish exposed to low salinity change (25 and 20 ppt) while in higher salinity change (5 ppt), the survival percentage was 50%.

Conclusion:

The study revealed that the serum cortisol concentration was high initially and continues to decrease to resting cortisol level at 120 min indicating that cortisol hormone is released following acute stress as a primary response in grouper juveniles.

Transcriptome analysis provides insights into the immune responsive pathways and genes in the head kidney of tiger grouper (Epinephelus fuscoguttatus) fed with Spatholobus suberectus, Phellodendron amurense, or Eclipta prostrata

The tiger grouper, Epinephelus fuscoguttatus, is an economically important fish in Southeast Asia but has been plagued by several diseases. Spatholobus suberectus (S), Phellodendron amurense (P), and Eclipta prostrate (E) are three commonly used Chinese medicinal herbs. Although previous pharmacological and clinical studies indicated that S, P, and E possess a variety of beneficial functions in mammals, little is known about their functions in farmed fish and the underlying molecular mechanism of their actions. Challenge tests in this study showed that after 14 days of diet supplement, all these herbs could effectively enhance the disease resistance of E. fuscoguttatus against Vibrio harveyi. However, the non-specific immune parameters of the herb-supplemented groups were not significantly different from the control group. To further explore the molecular mechanism of herbal immune-regulating effects on E. fuscoguttatus, transcriptome sequencing and RNA-Seq technique were applied on E. fuscoguttatus kidney. De novo transcriptome assembly of E. fuscoguttatus kidney yield 80,014 unigenes, among which, 44,901 (56.12%) were annotated with at least one of the public databases (Nr, Nt, Swiss-Prot, KEGG, COG, GO). Among these, 22,738, 11,700 and 27,457 unigenes were assigned to 57, 25 and 258 categories of GO, COG and KEGG databases, respectively. Using Solexa/Illumina's DGE platform, a total of 231, 186 and 144 putative differentially expressed genes (DEGs) were detected in P, E and S group compared with the control group. GO analysis indicated that in P and E, down-regulated DEGs were dominant in almost every GO term; whereas in S, up-regulated DEGs were more dominant. KEGG pathway analysis revealed that putative DEGs in all three herb groups were obviously enriched in the pathways related to infective diseases and immune system. We also identified a number of immune relative genes and pathways (TLR5, IL8 and MAPK pathway, for instance) associated with P, E and S's regulatory effects on E. fuscoguttatus. This study will enrich the E. fuscoguttatus transcriptome database, contribute to a better understanding of the molecular mechanisms associated with the immunoregulatory activities of Chinese medicinal herbs on teleost and provide valuable information on the prevention of grouper Vibrio diseases using Chinese medicinal herbs.

Successful sperm cryopreservation of the brown-marbled grouper, Epinephelus fuscoguttatus using propylene glycol as cryoprotectant

This study developed the cryopreservation of brown-marbled grouper spermatozoa for practical application. We examined 32 cryodiluents, developed from four types of cryoprotectants [propylene glycol (PG), dimethyl-sulphoxide (Me₂SO), dimethyl-acetamide (DMA) and ethylene glycol (EG)] at four concentrations of 5, 10, 15 and 20% in combination with two extenders [Fetal bovine serum (FBS) and artificial seminal plasma (ASP). Cooling rates were examined by adjusting the height of straws (2.5-12.5 cm) from the liquid nitrogen (LN) vapor and cooled for 5 min before immersion into LN. DNA laddering was used to detect DNA damage in cryopreserved sperm. In fertilization trials, 0.5 g of eggs was mixed with cryopreserved sperm stored for 30 days in LN. The best motility of post-thaw sperm was achieved using 15% PG + 85% FBS (76.7 ± 8.8%); 10% PG + 90% FBS was also effective as cryodiluent. Generally, FBS gave better post-thaw motility compared to ASP. The optimum cooling rate was at 17.6 °C min^-1 obtained by freezing at the height of 7.5 cm surface of LN. The results obtained showed that cryopreserved sperm of brown-marbled grouper suffered slight DNA fragmentation, which resulted in significantly lower motility. However, the fertilization (90.9 ± 0.5%), hatching (64.5 ± 4.1%) and deformity rates (3.8 ± 0.2%) obtained from cryopreserved sperm showed no significant difference with fresh sperm. These findings show that the developed protocol for cryopreservation of brown-marbled grouper sperm was viable and will be useful for successful breeding and seed production of brown-marbled grouper.

Transcriptome data of Epinephelus fuscoguttatus infected by Vibrio vulnificus

Vibriosis disease by Vibrio spp. greatly reduced productivity of aquaculture, such as brown-marbled grouper (Epinephelus fuscoguttatus), which is an economically important fish species in Malaysia. Preventive measures and immediate treatment are critical to reduce the mortality of E. fuscoguttatus from vibriosis. To investigate the molecular mechanisms associated with immune response and host-bacteria interaction, a transcriptomic analysis was performed to compare between healthy and Vibrio-infected groupers. This permits the discovery of immune-related genes, specifically the resistance genes upon infection. Herein, we provide the raw transcriptome data from Illumina HiSeq. 4000 that have been deposited into NCBI SRA database with the BioProject accession number PRJNA396437. A total of 493,403,076 raw sequences of 74.5 Gb were obtained. Trimming of the raw data produced 437,186,232 clean reads of ~58 Gb. These datasets will be useful to elucidate the defence mechanisms of E. fuscoguttatus against Vibrio vulnificus infection for future development of effective prevention and treatment of vibriosis.

Characterization of a vasa homolog in the brown-marbled grouper (Epinephelus fuscoguttatus) and its expression in gonad and germ cells during larval development

The vasa gene is specifically expressed in the germ cell lineage, and its expression has been used to study germline development in many organisms, including fishes. In this study, we cloned and characterized vasa as Efu-vasa in the brown-marbled grouper (Epinephelus fuscoguttatus). Efu-vasa contained predicted regions that shared consensus motifs with the vasa family in teleosts, including arginine- and glycine-rich repeats, ATPase motifs, and a DEAD box. Phylogenetic-tree construction using various DEAD-box proteins confirmed that Efu-vasa was clustered in the vasa family. Efu-vasa mRNA was detectable only in gonads, by reverse transcription polymerase chain reaction. Primordial germ cells (PGCs) during early gonad development in larvae were characterized by histological examination and in situ hybridization using an Efu-vasa antisense probe. Migrating PGCs were found in larvae at 9-21 days post-hatching, and rapid proliferation of PGCs was initiated in 36 days post-hatching. These findings provide a valuable basis for optimizing the developmental stages for germ cell transplantation in order to produce surrogate broodstock, which may help in the production of larvae of large and endangered grouper species.

Metagenomic analysis between free-living and cultured Epinephelus fuscoguttatus under different environmental conditions in Indonesian waters

In this study, we analyzed and compared feces of free-living and cultivated fish species, Epinephelus fuscoguttatus under different environmental conditions in Indonesian waters. Metagenome analysis was performed using Illumina MiSeq sequencing of the whole metagenomic DNA isolated from fish feces samples. The analysis covered both prokaryotic and eukaryotic DNA. Feces samples from mariculture fish revealed a highly stable distribution of several orders of bacteria when compared to samples from free-living fish, which were highly diverse and dominated by Vibrionales, Pseudomonales, Rhizobiales and non-classifiable Alphaproteobacteria. The eukaryotic content of the samples was dominated by residues of the host and nine additional fish species that formed a portion of the diet. Investigations on functional annotations for predominant bacterial taxa, using Gene Ontology enrichment, revealed a number of functions related to DNA metabolic processes, especially DNA repair, as well as antibiotic response in the free-living fish species.

Homogeneous Nature of Malaysian Marine Fish Epinephelus fuscoguttatus (Perciformes; Serranidae): Evidence Based on Molecular Markers, Morphology and Fourier Transform Infrared Analysis

Taxonomic confusion exists within the genus Epinephelus due to the lack of morphological specializations and the overwhelming number of species reported in several studies. The homogenous nature of the morphology has created confusion in the Malaysian Marine fish species Epinephelus fuscoguttatus and Epinephelus hexagonatus. In this study, the partial DNA sequence of the 16S gene and mitochondrial nucleotide sequences of two gene regions, Cytochrome Oxidase Subunit I and III were used to investigate the phylogenetic relationship between them. In the phylogenetic trees, E. fuscoguttatus was monophyletic with E. hexagonatus species and morphology examination shows that no significant differences were found in the morphometric features between these two taxa. This suggests that E. fuscoguttatus is not distinguishable from E. hexagonatus species, and that E. fuscoguttatus have been identified to be E. hexagonatus species is likely attributed to differences in environment and ability to camouflage themselves under certain conditions. Interestingly, this finding was also supported by Principal Component Analysis on Attenuated Total Reflectance-Fourier-transform Infrared (ATR-FTIR) data analysis. Molecular, morphological and meristic characteristics were combined with ATR-FTIR analysis used in this study offer new perspectives in fish species identification. To our knowledge, this is the first report of an extensive genetic population study of E. fuscoguttatus in Malaysia and this understanding will play an important role in informing genetic stock-specific strategies for the management and conservation of this highly valued fish.

The complete mitochondrial genome of the Epinephelus fuscoguttatus (Perciformes: Serranidae)

The complete mitochondrial genome of the Epinephelus fuscoguttatus was presented in this study. The mitochondrial genome is 16,648 bp long and consists of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region. The gene order and the composition of E. fuscoguttatus mitochondrial genome were similar to that of most other vertebrates. The nucleotide compositions of the light strand are 26.91% of A, 15.58% of C, 29.19% of T, and 28.32% of G. With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand.