Specific biomarkers and neurons distribution of different brain regions in largemouth bass (Micropterus salmoides).

The brain regulates multiple physiological processes in fish. Despite this, knowledge about the basic structure and function of distinct brain regions in non-model fish species remains limited due to their diversity and the scarcity of common biomarkers. In the present study, four major brain parts, the telencephalon, diencephalon, mesencephalon and rhombencephalon, were isolated in largemouth bass, Micropterus salmoides. Within these parts, nine brain regions and 74 nuclei were further identified through morphological and cytoarchitectonic analysis. Transcriptome analysis revealed a total of 7153 region-highly expressed genes and 176 region-specifically expressed genes. Genes related to growth, reproduction, emotion, learning, and memory were significantly overexpressed in the olfactory bulb and telencephalon (OBT). Feeding and stress-related genes were in the hypothalamus (Hy). Visual system-related genes were predominantly enriched in the optic tectum (OT), while vision and hearing-related genes were widely expressed in the cerebellum (Ce) region. Sensory input and motor output-related genes were in the medulla oblongata (Mo). Osmoregulation, stress response, sleep/wake cycles, and reproduction-related genes were highly expressed in the remaining brain (RB). Three candidate marker genes were further identified for each brain regions, such as neuropeptide FF (npff) for OBT, pro-melanin-concentrating hormone (pmch) for Hy, vesicular inhibitory amino acid transporter (viaat) for OT, excitatory amino acid transporter 1 (eaat1) for Ce, peripherin (prph) for Mo, and isotocin neurophysin (itnp) for RB. Additionally, the distribution of seven neurotransmitter-type neurons and five types of non-neuronal cells across different brain regions were analyzed by examining the expression of their marker genes. Notably, marker genes for glutamatergic and GABAergic neurons showed the highest expression levels across all brain regions. Similarly, the marker gene for radial astrocytes exhibited high expression compared to other markers, while those for microglia were the least expressed. Overall, our results provide a comprehensive overview of the structural and functional characteristics of distinct brain regions in the largemouth bass, which offers a valuable resource for understanding the role of central nervous system in regulating physiological processes in teleost.

DC-SIGN of Largemouth Bass (Micropterus salmoides) Mediates Immune Functions against Aeromonas hydrophila through Collaboration with the TLR Signaling Pathway.

C-type lectins in organisms play an important role in the process of innate immunity. In this study, a C-type lectin belonging to the DC-SIGN class of Micropterus salmoides was identified. MsDC-SIGN is classified as a type II transmembrane protein. The extracellular segment of MsDC-SIGN possesses a coiled-coil region and a carbohydrate recognition domain (CRD). The key amino acid motifs of the extracellular CRD of MsDC-SIGN in Ca2+-binding site 2 were EPN (Glu-Pro-Asn) and WYD (Trp-Tyr-Asp). MsDC-SIGN-CRD can bind to four pathogen-associated molecular patterns (PAMPs), including lipopolysaccharide (LPS), glucan, peptidoglycan (PGN), and mannan. Moreover, it can also bind to Gram-positive, Gram-negative bacteria, and fungi. Its CRD can agglutinate microbes and displays D-mannose and D-galactose binding specificity. MsDC-SIGN was distributed in seven tissues of the largemouth bass, among which the highest expression was observed in the liver, followed by the spleen and intestine. Additionally, MsDC-SIGN was present on the membrane of M. salmoides leukocytes, thereby augmenting the phagocytic activity against bacteria. In a subsequent investigation, the expression patterns of the MsDC-SIGN gene and key genes associated with the TLR signaling pathway (TLR4, NF-κB, and IL10) exhibited an up-regulated expression response to the stimulation of Aeromonas hydrophila. Furthermore, through RNA interference of MsDC-SIGN, the expression level of the DC-SIGN signaling pathway-related gene (RAF1) and key genes associated with the TLR signaling pathway (TLR4, NF-κB, and IL10) was decreased. Therefore, MsDC-SIGN plays a pivotal role in the immune defense against A. hydrophila by modulating the TLR signaling pathway.

Estradiol-17ß and bisphenol A affect growth and mineralization in early life stages of seabass.

Natural and synthetic estrogens are contaminants present in aquatic ecosystems. They can have significant consequences on the estrogen-sensitive functions of organisms, including skeletal development and growth of vertebrate larvae. Synthetic polyphenols represent a group of environmental xenoestrogens capable of binding the receptors for the natural hormone estradiol-17ß (E2). To better understand how (xeno-)estrogens can affect the skeleton in fish species with high ecological and commercial interest, 16 days post-hatch larvae of the seabass were experimentally exposed for 7 days to E2 and Bisphenol A (BPA), both used at the regulatory concentration of surface water quality (E2: 0.4 ng.L-1, BPA: 1.6 µg.L-1) or at a concentration 100 times higher. Skeletal mineralization levels were evaluated using Alizarin red staining, and expression of several genes playing key roles in growth, skeletogenesis and estrogen signaling pathways was assessed by qPCR. Our results show that E2 exerts an overall negative effect on skeletal mineralization at the environmental concentration of 0.4 ng.L-1, correlated with an increase in the expression of genes associated only with osteoblast bone cells. Both BPA exposures inhibited mineralization with less severe effects and modified bone homeostasis by regulating the expression of gene encoding osteoblasts and osteoclasts markers. Our results demonstrate that environmental E2 exposure inhibits larval growth and has an additional inhibitory effect on skeleton mineralization while both BPA exposures have marginal inhibitory effect on skeletal mineralization. All exposures have significant effects on transcriptional levels of genes involved in the skeletal development of seabass larvae.

Molecular characterization of vascular endothelial growth factor b from spotted sea bass (Lateolabrax maculatus) and its potential roles in decreasing lipid deposition.

Vascular endothelial growth factor B (VEGFB), a member of the VEGF family, exhibits limited angiogenic activity in mammals but plays an unexpected role in targeting lipids to peripheral tissues. However, its role in lipid metabolism in fish is unknown. In this study, the vegfb gene was cloned and characterized from spotted sea bass (Lateolabrax maculatus). It encodes 254 amino acids and possesses the typical characteristics of the Vegfb family, demonstrating high homology with those from other vertebrate species. The vegfb gene exhibits the highest expression levels in the liver, followed by the gills, intestine, and adipose tissues in spotted sea bass. In vivo, high-lipid diets decreased vegfb expression and increased lipid deposition in liver of fish. In vitro, palmitic acid + oleic acid treatment or vegfb knockdown significantly increased TG and TC contents, promoting lipid droplet deposition in hepatocytes. Vegfb overexpression has the opposite effects, inhibiting lipid deposition and downregulating fatty acid transport and adipogenesis genes. In contrast, the vegfb knockdown significantly upregulated the expression levels of c/ebpα, plin2, and dgat1 (P < 0.05). These results demonstrate that Vegfb may play an important role in reducing lipid deposition by regulating fatty acid transport and adipogenesis in the hepatocytes of spotted sea bass.

Occurrence of microplastics and metals in European seabass produced in different aquaculture systems: Implications for human exposure, risk, and food safety.

Microplastics (MPs) are emerging contaminants of increasing concern as they may cause adverse effects and carry other contaminants, which may potentially compromise human health. Despite occurring in aquatic ecosystems worldwide, the knowledge about MP presence in different aquaculture systems and their potential impact on seafood products is still limited. This study aimed to determine the levels of MPs in water, feed, and European seabass (Dicentrarchus labrax) from three relevant aquaculture systems and estimate human exposure to MPs and metals through seabass consumption. The recirculating aquaculture system (RAS) had the highest MP occurrence in water and feed. MP levels in seabass followed the aquaculture system's levels in water and feed, with RAS-farmed fish presenting the highest MP load, both in the fish gastrointestinal tract (GIT) and muscle, followed by pond-, and cage-farmed fish. MPs' characteristics across aquaculture systems and fish samples remained consistent, with the predominant recovered particles falling within the MP size range. The particles were visually characterized and chemically identified by micro-Fourier Transform Infrared Spectroscopy (µFTIR). Most of these particles were fibres composed of man-made cellulose and PET. MP levels in GIT were significantly higher than in muscle for pond- and RAS-farmed fish, MPs' bioconcentration factors >1 indicated bioconcentration in farmed seabass. Metal concentrations in fish muscle were below permissible limits, posing low intake risks for consumers according to the available health-based guidance values and estimated dietary scenarios.

Effects of Long-Term Cryopreservation on the Transcriptomes of Giant Grouper Sperm.

The giant grouper fish (Epinephelus lanceolatus), one of the largest and rarest groupers, is a fast-growing economic fish. Grouper sperm is often used for cross-breeding with other fish and therefore sperm cryopreservation is important. However, freezing damage cannot be avoided. Herein, we performed a transcriptome analysis to compare fresh and frozen sperm of the giant grouper with frozen storage times of 0, 23, 49, and 61 months. In total, 1911 differentially expressed genes (DEGs), including 91 in El-0-vs-El-23 (40 upregulated and 51 downregulated), 251 in El-0-vs-El-49 (152 upregulated and 69 downregulated), and 1569 in El-0-vs-El-61 (984 upregulated and 585 downregulated), were obtained in the giant grouper sperm. DEGs were significantly increased at 61 months of cryopreservation (p < 0.05). GO and KEGG enrichment analyses of the DEGs revealed significant enrichment in the pilus assembly, metabolic process, MAPK signaling pathway, apoptosis, and P53 signaling pathway. Time-series expression profiling of the DEGs showed that consistently upregulated modules were also significantly enriched in signaling pathways associated with apoptosis. Four genes, scarb1, odf3, exoc8, and atp5f1d, were associated with mitochondria and flagella in a weighted correlation network analysis. These genes may play an important role in the response to sperm freezing. The experimental results show that long-term cryopreservation results in freezing damage to the giant grouper sperm. This study provides rich data for studies of the mechanism underlying frozen fish sperm damage as well as a technical reference and evaluation index for the long-term cryopreservation of fish sperm.

Karyotypic changes and diversification time in Epinephelidae groupers (Perciformes). Implications on reproductive isolation.

Groupers (Epinephelidae and Serranidae) have attracted special attention to fish farming, and their species offer good opportunities for successful hybridizations. Cytogenetic data allow a better understanding of the role of karyotypic diversification in the acquisition of post-zygotic reproductive isolation (RI). Thus, chromosomal analyses were performed on E. striatus (Caribbean Sea), E. coioides and E. tauvina (Indo-Pacific Region), using standard procedures and mapping of six repetitive DNA classes by the in situ hybridization. The three species have 2n=48 chromosomes. The karyotypes of E. coioides and E. striatus are composed only of acrocentric chromosomes (FN=48), while E. tauvina has 8 submetacentric chromosomes (FN=56). Heterochromatin has a preferential centromeric distribution, and the microsatellite repeats are dispersed throughout the chromosomes of all species. The 18S and 5S rDNA sites are unique but show a colocalization arrangement in E. tauvina and E. striatus. The chromosomal organization suggests that the three species still maintain a significant amount of syntenic regions. The range of the karyotype divergence and the RI levels showed low, but goes turn proportionally greater in relation to the divergence time between the parental species. The slow acquisition of postzygotic RI is consistent with the high karyotype homogeneity presented by Epinephelidae family.

Natural zeolite for heavy metal, ammonia removal, and physiological responses in European sea bass (Dicentrarchus labrax) juveniles tanks with different densities.

The present study aims to investigate the influence of zeolite usage and stocking densities on various parameters, including ammonia removal from water, accumulation of heavy metals in fish organs, water quality, growth performance, feed efficiency, muscle composition, as well as hematological and biochemical parameters in European seabass (Dicentrarchus labrax) over a 90-day duration. A total of 2400 D. labrax with an initial weight of 9.83 ± 2.02 g and initial length of 9.37 ± 0.32 cm were distributed among 24 tanks. The research involved six distinct treatment groups, with two different zeolite levels (0 and 15 ppt) and three stocking density levels (50, 100, and 150 fish/m3), each replicated four times. The results of the research demonstrate a statistically significant improvement (p < 0.05) in water quality measures with the introduction of zeolite. The successful implementation of this amendment mitigated the adverse effects of fish density on water quality parameters. Higher stocking density negatively impacted European sea bass growth, feed utilization, and hemato-biochemical indicators. Zeolite use effectively alleviated these adverse effects, particularly on performance, feed utilization, hematological, and biochemical parameters. The study's results indicate that the utilization of zeolite has shown to be efficacious in mitigating the accumulation of heavy metals in both water and fish organs, while concurrently augmenting fish attributes. However, the increase in density led to a significant decrease in the accumulation of heavy metals in both water and fish organs. The present study highlights the capacity of natural zeolites to mitigate the negative consequences associated with water quality concerns. The efficiency of these zeolites in limiting the accessibility of heavy metals in polluted water is shown, hence minimizing their accumulation in fish organs. In addition, the improvement of fish performance has the capacity to have a beneficial influence on both the well-being and efficiency of fish in aquaculture. Additional research is essential to fully understand the complex molecular pathways involved in utilizing natural zeolite under different fish densities.

Physiological responses of European sea bass (Dicentrarchus labrax) exposed to increased carbon dioxide and reduced seawater salinities.

BACKGROUND: The iono- and osmoregulatory capacities of marine teleosts, such as European sea bass (Dicentrarchus labrax) are expected to be challenged by high carbon dioxide exposure, and the adverse effects of elevated CO2 could be amplified when such fish migrate into less buffered hypo-osmotic estuarine environments. Therefore, the effects of increased CO2 on the physiological responses of European sea bass (Dicentrarchus labrax) acclimated to 32 ppt, 10 ppt and 2.5 ppt were investigated. METHODS: Following acclimation to different salinities for two weeks, fish were exposed to present-day (400 µatm) and future (1000 µatm) atmospheric CO2 for 1, 3, 7 and 21 days. Blood pH, plasma ions (Na+, K+, Cl-), branchial mRNA expression of ion transporters such as Na+/K+-ATPase (NKA), Na+/K+/2Cl- co-transporters (NKCC) and ammonia transporters (e.g. Rhesus glycoproteins Rhbg, Rhcg1 and Rhcg2) were examined to understand the iono- and osmoregulatory consequences of elevated CO2. RESULTS: A transient but significant increase in the blood pH of exposed fish acclimated at 10 ppt (day 1) and 2.5 ppt (day 21) was observed possibly due to an overshoot of the blood HCO3- accumulation while a significant reduction of blood pH was observed after 21 days at 2.5ppt. However, no change was seen at 32 ppt. Generally, Na + concentration of control fish was relatively higher at 10 ppt and lower at 2.5 ppt compared to 32 ppt control group at all sampling periods. Additionally, NKA was upregulated in gill of juvenile sea bass when acclimated to lower salinities compared to 32 ppt control group. CO2 exposure generally downregulated NKA mRNA expression at 32ppt (day 1), 10 ppt (days 3, 7 and 21) and 2.5ppt (days 1 and 7) and also a significant reduction of NKCC mRNA level of the exposed fish acclimated at 32 ppt (1-3 days) and 10 ppt (7-21 days) was observed. Furthermore, Rhesus glycoproteins were generally upregulated in the fish acclimated at lower salinities indicating a higher dependance on gill ammonia excretion. Increased CO2 led to a reduced expression of Rhbg and may therefore reduce ammonia excretion rate. CONCLUSION: Juvenile sea bass were relatively successful in keeping acid base balance under an ocean acidification scenario. However, this came at a cost for ionoregulation with reduced NKA, NKCC and Rhbg expression rates as a consequence.

Functional characterization of Malabar grouper (Epinephelus malabaricus) interferon regulatory factor 9 involved in antiviral response.

IRF9 is a crucial component in the JAK-STAT pathway. IRF9 interacts with STAT1 and STAT2 to form IFN-I-stimulated gene factor 3 (ISGF3) in response to type I IFN stimulation, which promotes ISG transcription. However, the mechanism by which IFN signaling regulates Malabar grouper (Epinephelus malabaricus) IRF9 is still elusive. Here, we explored the nd tissue-specific mRNA distribution of the MgIRF9 gene, as well as its antiviral function in E. malabaricus. MgIRF9 encodes a protein of 438 amino acids with an open reading frame of 1317 base pairs. MgIRF9 mRNA was detected in all tissues of a healthy M. grouper, with the highest concentrations in the muscle, gills, and brain. It was significantly up-regulated by nervous necrosis virus infection and poly (I:C) stimulation. The gel mobility shift test demonstrated a high-affinity association between MgIRF9 and the promoter of zfIFN in vitro. In GK cells, grouper recombinant IFN-treated samples showed a significant response in ISGs and exhibited antiviral function. Subsequently, overexpression of MgIRF9 resulted in a considerable increase in IFN and ISGs mRNA expression (ADAR1, ADAR1-Like, and ADAR2). Co-immunoprecipitation studies demonstrated that MgIRF9 and STAT2 can interact in vivo. According to the findings, M. grouper IRF9 may play a role in how IFN signaling induces ISG gene expression in grouper species.

A nanobody-mediated drug system against largemouth bass virus delivered by bacterial nanocellulose in Micropterus salmoides.

Diseases caused by pathogens severely hampered the development of aquaculture, especially largemouth bass virus (LMBV) has caused massive mortality and severe economic losses to the culture of largemouth bass (Micropterus salmoides). Considering the environmental hazards and human health, effective and environmentally friendly therapy strategy against LMBV is of vital importance and in pressing need. In the present study, a novel nanobody (NbE4) specific for LMBV was selected from a phage display nanobody library. Immunofluorescence and indirect ELISA showed that NbE4 could recognize LMBV virions and had strong binding capacity, but RT-qPCR evidenced that NBE4 did not render the virus uninfectious. Besides, antiviral drug ribavirin was used to construct a targeted drug system delivered by bacterial nanocellulose (BNC). RT-qPCR revealed that NbE4 could significantly enhance the antiviral activity of ribavirin in vitro and in vivo. The targeted drug delivery system (BNC-Ribavirin-NbE4, BRN) reduced the inflammatory response caused by LMBV infection and improved survival rate (BRN-L, 33.3 %; BRN-M, 46.7 %; BRN-H, 56.7 %)compared with control group (13.3 %), ribavirin group (RBV, 26.7 %) and BNC-ribavirin (BNC-R, 40.0 %), respectively. This research provided an effective antiviral strategy that improved the drug therapeutic effect and thus reduced the dosage.

Differing physiological performance of coexisting cool- and warmwater fish species under heatwaves in the Midwestern United States.

Heatwaves are becoming more frequent and intensified with climate change. Freshwater ecosystems are among the most threatened, within which, differing responses between cool- and warmwater species to heatwaves can lead to fundamental changes in communities. Physiological experiments can identify potential mechanisms underlying the impacts of such heatwaves on fish communities. In the current study, we quantified the oxygen consumption rate, aerobic scope and swimming performance of cool- and warmwater fish species following the simulation of short-term heatwaves currently occurring in streams in the Midwestern United States. The coolwater predator walleye (Sander vitreus) showed clear thermal disadvantages relative to the warmwater predator largemouth bass (Micropterus salmoides), based on a high metabolic cost during the heatwave, low metabolic activity when encountering prey, and reduced swimming performance following the heatwave. Largemouth bass also showed a thermal advantage relative to the warmwater prey fathead minnow (Pimephales promelas) related to swimming performance and energetic costs, highlighting differing thermal responses between predators and prey. This study demonstrates the importance of considering short-term extreme thermal events in the response of aquatic communities to climate stressors.

The Effects of Wastewater Reuse on Smallmouth Bass (Micropterus dolomieu) Relative Abundance in the Shenandoah River Watershed, USA.

Municipal and industrial wastewater effluent is an important source of water for lotic systems, especially during periods of low flow. The accumulated wastewater effluent flows-expressed as a percentage of total streamflow (ACCWW%)-contain chemical mixtures that pose a risk to aquatic life; fish may be particularly vulnerable when chronically exposed. Although there has been considerable focus on individual-level effects of exposure to chemical mixtures found in wastewater effluent, scaling up to population-level effects remains a challenging component needed to better understand the potential consequences of exposure in wild populations. This may be particularly important under a changing climate in which wastewater reuse could be essential to maintain river flows. We evaluated the effects of chronic exposure to wastewater effluent, as measured by ACCWW%, on the relative abundance of young-of-year (YOY), juvenile, and adult smallmouth bass (Micropterus dolomieu) populations in the Shenandoah River Watershed (USA). We found that increases in ACCWW% in the previous year and during the prespawn period were negatively correlated with the relative abundance of YOY, resulting in an average 41% predicted decrease in abundance (range = 0.5%-94% predicted decrease in abundance). This lagged effect suggests that adult fish reproductive performance may be compromised by chemical exposure during periods of high ACCWW%. No relationships between ACCWW% and juvenile or adult relative abundance were found, suggesting that negative effects of ACCWW% on YOY abundance may be offset due to compensatory mechanisms following higher ACCWW% exposure. Understanding the effects of wastewater effluent exposure at multiple levels of biological organization will help in the development of management strategies aimed at protecting aquatic life. Environ Toxicol Chem 2024;43:1138-1148. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Liver histopathological and oxidative stress assessment by a combination of formaldehyde and oxytetracycline in sea bass (Dicentrarchuslabrax L).

Background: Formaldehyde (FA) and oxytetracycline (OTC) are the chemicals commonly used in aquaculture to prevent or treat fish diseases due to protozoa, parasites, and bacteria. Aim: The goal of the present study is to assess the liver injury and oxidative stress induced by exposure of sea bass (Dicentrarchuslabrax L) to therapeutic doses of FA (200 ml.m-3) and OTC (40 g.m-3) under the same conditions being applied in intensive aquaculture systems in Tunisia. Methods: The liver histopathological survey was achieved after 5 and 10 days of exposure to FA, OTC separately or mixed. In parallel, liver catalase activity and malondialdehyde (MDA) were measured to assess oxidative stress. Results: Results showed that treatment with FA and OTC used alone or in combinations induced liver damage as measured by sinusoid dilatation, intensive vacuolization, blood congestion, and focal necrosis. Significant elevation in catalyze activity and MDA levels were also observed in liver homogenates by the treatment (p ≤ 005). Conclusion: Combined treatment induced higher effects suggesting the critical hazards associated with FA and OTC when released to the environment.

Development and characterization of 40 InDel markers from the major histocompatibility complex genes of largemouth bass (Micropterus salmoides).

BACKGROUND: The genetic improvement in growth and food habit domestication of largemouth bass (Micropterus salmoides) have made breakthroughs in past decades, while the relevant work on disease resistance were rarely carried out. Major histocompatibility complex (MHC) genes, which are well known as their numbers and high polymorphisms, have been used as candidate genes to mine disease-resistant-related molecular markers in many species. METHODS AND RESULTS: In present study, we developed and characterized 40 polymorphic and biallelic InDel markers from the major histocompatibility complex genes of largemouth bass. The minor allele frequency, observed heterozygosity, expected heterozygosity and polymorphic information content of these markers ranged from 0.0556 to 0.5000, 0.1111 to 0.6389, 0.1064 to 0.5070, and 0.0994 to 0.3750, respectively. Three loci deviated significantly from Hardy-Weinberg equilibrium, while linkage disequilibrium existed at none of these loci. CONCLUSION: These InDel markers might provide references for the further correlation analysis and molecular assisted selection of disease resistance in largemouth bass.

Spatial and ontogenetic modulation of fatty acid composition in juvenile European sea bass (Dicentrarchus labrax) from two French estuaries.

This study evaluated how estuary of origin and ontogenetic stage influence the fatty acid (FA) composition in the tissues of wild European sea bass juvenile. We evidenced tissue-specific patterns, with the brain exhibiting a distinct FA composition from the liver and muscle. Ontogenetic stage and estuary influenced the general FA profile, and particularly the essential FA (EFA) like docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and arachidonic acid (ARA) in all tissues. The data also revealed the ability of wild sea bass to modulate, at the molecular level, FA biosynthesis pathways and suggest a potential dietary DHA limitation in the natural environment. The distribution of FA within tissues might reflect shifts in diet, metabolic demands, or adaptations to environmental conditions. This study provides insights about FA dynamics in euryhaline fish during juvenile life stage, improving our understanding of the metabolism need and EFA trophic availability in a changing environment.

Physicochemical variables influencing the abundance of Atlantic goliath grouper juveniles (Epinephelus itajara) in a tropical Brazilian mangrove habitat.

The purpose of this study was to investigate the relationships between the abundance and occurrence of juvenile Atlantic goliath grouper and physicochemical variables in a tropical mangrove ecosystem, employing a non-lethal methodology. Juvenile Atlantic goliath grouper individuals were captured biweekly, using blue crab traps, across three locations within the São Mateus estuary (18°36'S, 39°44'W), from August 2021 to July 2022. Simultaneously, the physicochemical water variables were assessed during each trap inspection. The physicochemical water variables influence on the abundance and occurrence of Atlantic goliath grouper juveniles were assessed using the Zero-Inflated Binomial (ZIB) and the Poisson (ZIP) generalized linear mixed-effects models (GLMMs). A total of 66 Atlantic goliath grouper juveniles were sampled (Pontal do Sul = 50, Lagoa Creek = 13, and Pitangueiras Creek = 3), ranging from 32 to 319 mm in total length. The best model fitted to presence-absence data (AIC = 278.6) consisted of location, depth, and salinity, with only location having a significant influence on the likelihood of species occurrence. Regarding abundance data, the best model (AIC = 336.4) included location, depth, and turbidity, with only location and depth showing a significant impact on abundance variation, with lower abundance at deeper areas. Although our results indicate a weak significant influence of physicochemical variables on juvenile Atlantic goliath grouper distribution, it is imperative to continue this monitoring effort, considering that additional data may be required to gain a deeper understanding of these patterns.

In-depth discovery and taste presentation mechanism studies on umami peptides derived from fermented sea bass based on peptidomics and machine learning.

Umami peptides originating from fermented sea bass impart a distinctive flavor to food. Nevertheless, large-scale and rapid screening for umami peptides using conventional techniques is challenging because of problems such as prolonged duration and complicated operation. Therefore, we aimed to screen fermented sea bass using peptidomics and machine learning approaches. The taste presentation mechanism of umami peptides was assessed by molecular docking of T1R1/T1R3. Seventy umami peptides identified in fermented sea bass predominantly originated from 28 precursor proteins, including troponin, myosin, motor protein, and creatine kinase. Six umami peptides with the lowest energies formed stable complexes by binding to T1R3. SER170, SER147, GLN389, and HIS145 are critical binding sites for T1R1/T1R3. Four dominant interacting surface forces were identified: aromatic interactions, hydrogen bonding, hydrophilic bonds, and solvent-accessible surfaces. Our study unveils a method to screen umami peptides efficiently, providing a basis for further exploration of their flavor in fermented sea bass.

Genetic mechanism of body size variation in groupers: Insights from phylotranscriptomics.

Animal body size variation is of particular interest in evolutionary biology, but the genetic basis remains largely unknown. Previous studies have shown the presence of two parallel evolutionary genetic clusters within the fish genus Epinephelus with evident divergence in body size, providing an excellent opportunity to investigate the genetic basis of body size variation in vertebrates. Herein, we performed phylotranscriptomic analysis and reconstructed the phylogeny of 13 epinephelids originating from the South China Sea. Two genetic clades with an estimated divergence time of approximately 15.4 million years ago were correlated with large and small body size, respectively. A total of 180 rapidly evolving genes and two positively selected genes were identified between the two groups. Functional enrichment analyses of these candidate genes revealed distinct enrichment categories between the two groups. These pathways and genes may play important roles in body size variation in groupers through complex regulatory networks. Based on our results, we speculate that the ancestors of the two divergent groups of groupers may have adapted to different environments through habitat selection, leading to genetic variations in metabolic patterns, organ development, and lifespan, resulting in body size divergence between the two locally adapted populations. These findings provide important insights into the genetic mechanisms underlying body size variation in groupers and species differentiation.

Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper ( Plectropomus leopardus).

The leopard coral grouper ( Plectropomus leopardus) is a species of significant economic importance. Although artificial cultivation of P. leopardus has thrived in recent decades, the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data. In this study, we identified over 8.73 million single nucleotide polymorphisms (SNPs) through whole-genome resequencing of 326 individuals spanning six distinct groups. Furthermore, we categorized 226 individuals with high-coverage sequencing depth (≥14×) into eight clusters based on their genetic profiles and phylogenetic relationships. Notably, four of these clusters exhibited pronounced genetic differentiation compared with the other populations. To identify potentially advantageous loci for P. leopardus, we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity ( θπ) and fixation index ( F ST) in these four clusters. Using these high-coverage resequencing data, we successfully constructed the first haplotype reference panel specific to P. leopardus. This achievement holds promise for enabling high-quality, cost-effective imputation methods. Additionally, we combined low-coverage sequencing data with imputation techniques for a genome-wide association study, aiming to identify candidate SNP loci and genes associated with growth traits. A significant concentration of these genes was observed on chromosome 17, which is primarily involved in skeletal muscle and embryonic development and cell proliferation. Notably, our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs, showing potential for genetic selective breeding efforts. These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P. leopardus.