Fishes

20 pages, 4258 KB

Open AccessArticle

Impact of Stress Coping Styles on Serum Protein Electrophoresis Pattern Modulation in Sparus aurata Following Vibrio anguillarum Inoculation

by Mariele Staropoli, Mariano Dara, Irene Vazzana, Pierluigi Carbonara, Claudia La Corte, Luca Bisanti, Federica Bertini, Lucia Therese Marcianò, Daniela Parrinello, Maria Giovanna Parisi and Matteo Cammarata

Fishes 2026, 11(1), 70; https://doi.org/10.3390/fishes11010070 - 22 Jan 2026

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Abstract

Stress coping style (SCS) is crucial for animal welfare in the context of breeding. The link between behavioural traits and physiological responses to external stimuli is increasingly recognized and could orient the selection of appropriate SCSs for welfare-oriented breeding. This study aimed to [...] Read more.

Stress coping style (SCS) is crucial for animal welfare in the context of breeding. The link between behavioural traits and physiological responses to external stimuli is increasingly recognized and could orient the selection of appropriate SCSs for welfare-oriented breeding. This study aimed to evaluate how SCS influences the physiological responses of Sparus aurata, a widely used species in aquaculture, following Vibrio anguillarum stimulation. To this end, the serum protein electrophoretic profile, analysed by capillary electrophoresis, was used as an innovative parameter to assess physiological variations. S. aurata individuals were categorized into three SCS groups—bold, shy, and intermediate —based on a risk-taking test. Serum was collected at day 0 (pre-inactivated V. anguillarum inoculation) and at 30 and 60 days post-inoculation. Analyses revealed an increase in the β₂-globulin fraction, putatively associated with molecules involved in the physiological response following inactivated pathogen inoculation, accompanied by a decrease in the γ fraction over time. This trend was particularly pronounced in bold fish, while shy ones showed a similar but less marked pattern. Overall, the results suggest that proactive individuals exhibit a more marked physiological modulation to inactivated pathogen stimulation than reactive ones, highlighting modulation of serum protein electrophoresis as a sensitive bioindicator of physiological response in S. aurata. Full article

(This article belongs to the Special Issue Welfare and Stressor in Aquaculture: Mechanisms, Management, and Sustainable Solutions)

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20 pages, 1574 KB

Open AccessArticle

Impact of Extreme Climate Risk on Chinese Freshwater Aquaculture Production

by Yingli Zhang, Hang Qu and Shunxiang Yang

Fishes 2026, 11(1), 69; https://doi.org/10.3390/fishes11010069 - 22 Jan 2026

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Abstract

Against the backdrop of global warming and an increase in extreme weather events, the freshwater aquaculture industry, which is highly dependent on environmental conditions, faces severe challenges. As the world’s largest producer of freshwater aquaculture, the stability of China’s production is crucial for [...] Read more.

Against the backdrop of global warming and an increase in extreme weather events, the freshwater aquaculture industry, which is highly dependent on environmental conditions, faces severe challenges. As the world’s largest producer of freshwater aquaculture, the stability of China’s production is crucial for ensuring national food security and rural livelihoods. This study utilizes provincial panel data from China (2007–2023) and employs the HP filter separately for each province to construct a “climate-induced output” indicator. A panel data model is then established to examine the impact and transmission mechanisms of extreme climate risks on freshwater aquaculture output. The findings reveal the following: (1) Climate risks exert a significant negative impact on freshwater aquaculture production, with extreme low temperatures, droughts, and extreme rainfall having particularly pronounced effects. (2) Natural disasters play a partial mediating role between extreme climate and output, accounting for approximately 26.35% of the total effect. (3) From an overall perspective, both increased labor productivity and greater operational scale can significantly mitigate the negative impacts of climate risks. This study provides empirical evidence to inform policies on optimizing regional aquaculture layouts, enhancing climate resilience, and formulating adaptive strategies. Full article

(This article belongs to the Special Issue Impact of Climate Change and Adverse Environments on Aquaculture)

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16 pages, 1170 KB

Open AccessArticle

Geographical Traceability of Anguilla japonica from Different Habitats Successfully Achieved Using Muscle Elemental Fingerprint Analysis

by Chao Song, Chengyao Yang, Yijia Li, Dongyu Song, Xiaorong Huang, Sikai Wang, Feng Zhao and Hong Tao

Fishes 2026, 11(1), 68; https://doi.org/10.3390/fishes11010068 - 22 Jan 2026

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Abstract

Anguilla japonica is a catadromous fish, and the Yangtze River Estuary serves as a crucial passage for A. japonica migrating downstream to the sea. A large number of adult A. japonica appear on the market during the peak migration period. Due to the [...] Read more.

Anguilla japonica is a catadromous fish, and the Yangtze River Estuary serves as a crucial passage for A. japonica migrating downstream to the sea. A large number of adult A. japonica appear on the market during the peak migration period. Due to the lack of effective discrimination basis, it is difficult to distinguish the source of samples in market supervision. Therefore, there is an urgent need to trace the origin of A. japonica from different water bodies. This study analyzed muscle elemental fingerprints of 21 elements to determine the geographical origin of A. japonica. The results showed that A. japonica from different habitats had distinct elemental compositions in their muscles. Specifically, A. japonica from estuary waters (EW) was characterized by significantly higher levels of V and Hg compared to other water bodies. Na was identified as a key discriminant element among different habitats, with its content significantly increasing in river waters (RW), EW, and offshore waters (OW), respectively. Discriminant analysis selected four discriminant elements (V, Hg, Na and Cu) from 21 elemental compositions, among which V, Hg, and Na were the three key distinguishing elements. Based on the composition of these four discriminant elements in the muscles of A. japonica from different habitats, hierarchical cluster analysis (HCA), orthogonal partial least squares discriminant analysis (OPLS-DA), and linear discriminant analysis (LDA) were applied and validated, successfully achieving rapid and accurate origin tracing and verification for new samples, achieving 100% classification accuracy. Therefore, the application of muscle EFA can achieve the geographical traceability of A. japonica from different habitats. The analytical method and verification process for origin tracing established in this study can be successfully applied to market supervision for tracing the origin of samples with unknown sources. Full article

(This article belongs to the Special Issue Conservation and Population Genetics of Fishes)

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20 pages, 9876 KB

Open AccessArticle

The Effects of Dietary Tributyrin Supplementation on Growth Performance, Antioxidant Capacity, Immune Function, and Intestinal Health of Fat Greenling (Hexagrammos otakii)

by Yuepeng Song, Zijun Wei, Xinghao Li, Zheng Zhang, Yong Wang, Jichuan Du, Kewei Wang, Yike Li, Xuejie Li, Dongwei Li, Wei Wang and Yan Chen

Fishes 2026, 11(1), 67; https://doi.org/10.3390/fishes11010067 - 21 Jan 2026

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Abstract

The objective of the current research was to evaluate the influence of dietary tributyrin (TB) inclusion on the growth performance and physiological well-being of Hexagrammos otakii. Juvenile fish (initial weight 24.01 ± 1.35 g) were fed one of six isonitrogenous and isolipidic [...] Read more.

The objective of the current research was to evaluate the influence of dietary tributyrin (TB) inclusion on the growth performance and physiological well-being of Hexagrammos otakii. Juvenile fish (initial weight 24.01 ± 1.35 g) were fed one of six isonitrogenous and isolipidic diets containing graded levels of TB (0–1.5 g/kg) for 90 days. Supplementation significantly enhanced the weight gain and specific growth rates. The optimal level of 0.9 g/kg TB improved muscle nutritional quality, muscle texture, and intestinal morphology. This dosage also significantly increased hepatic and intestinal antioxidant capacity, elevating superoxide dismutase (SOD), catalase (CAT), and total antioxidant capacity (T-AOC), while reducing malondialdehyde (MDA) content. Furthermore, dietary TB at 0.9 g/kg reduced plasma and hepatic triglycerides and total cholesterol, and elevated key plasma immune parameters, including complement components (C3, C4) and phosphatase activities (ACP, AKP). Intestinal health was further enhanced, as evidenced by increased digestive enzyme activities (amylase, lipase, chymotrypsin) and improved microbial diversity, marked by a proliferation of beneficial bacteria. In conclusion, dietary TB supplementation at 0.9 g/kg optimally promotes growth, improves muscle and intestinal health, and enhances antioxidant and immune functions in H. otakii. Full article

(This article belongs to the Special Issue Dietary Supplementation in Aquaculture)

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15 pages, 1433 KB

Open AccessArticle

Biological Validation of Cortisol in Zebrafish Trunk, Skin Mucus, and Water as a Biomarker of Acute or Chronic Stress

by Sara Jorge, Luís Félix, Benjamín Costas, Lourenço Ramos-Pinto, Sofia R. Teixeira and Ana M. Valentim

Fishes 2026, 11(1), 66; https://doi.org/10.3390/fishes11010066 - 21 Jan 2026

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Abstract

The most used technique to assess cortisol in zebrafish is trunk sampling, a terminal procedure. Extracting cortisol non-terminally in adult zebrafish remains challenging, limiting longitudinal studies, and the reduction of the number of zebrafish used in research. This study explored non-terminal methods for [...] Read more.

The most used technique to assess cortisol in zebrafish is trunk sampling, a terminal procedure. Extracting cortisol non-terminally in adult zebrafish remains challenging, limiting longitudinal studies, and the reduction of the number of zebrafish used in research. This study explored non-terminal methods for cortisol measurement in adult zebrafish under acute and chronic stress, focusing on housing water and skin mucus as alternatives to terminal trunk sampling. Oxidative stress markers (cerebral and hepatic) were also assessed to confirm stress responses. In experiment A, zebrafish were exposed to no stress, acute stress (AS), or chronic stress for 14 days (CS14) to evaluate skin mucus and trunk cortisol as biomarkers. In experiment B, in addition to CS14, a 7-day unpredictable chronic stress protocol (CS7) was tested to discard stress habituation. Results showed significant effects on cerebral oxidative stress: AS increased ROS and AChE activity, CS7 reduced GPx and AChE, and CS14 raised GPx in experiment A, while it increased protein carbonyls and decreased ATPase levels in experiment B. Trunk and skin mucus cortisol increased following AS. Under chronic stress, trunk and skin mucus cortisol levels were not significantly altered, but water cortisol increased at CS7. In conclusion, skin mucus and trunk cortisol levels are reliable biomarkers for acute stress, while water cortisol holds promise for chronic stress. Full article

(This article belongs to the Section Physiology and Biochemistry)

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12 pages, 2758 KB

Open AccessArticle

Cooperative Associations Between Fishes and Bacteria: The Influence of Different Ocean Fishes on the Gut Microbiota Composition

by Jintao Liu, Bilin Liu, Yang Liu and Yuli Wei

Fishes 2026, 11(1), 65; https://doi.org/10.3390/fishes11010065 - 21 Jan 2026

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Abstract

Gut microbial communities perform a multitude of physiological functions for their hosts; however, the drivers and distribution patterns of microbiota in wild animals remain largely underexplored. Our understanding of how these microbial communities are structured across hosts in natural environments—especially within a single [...] Read more.

Gut microbial communities perform a multitude of physiological functions for their hosts; however, the drivers and distribution patterns of microbiota in wild animals remain largely underexplored. Our understanding of how these microbial communities are structured across hosts in natural environments—especially within a single host species remains limited. Here, we characterized the gut microbial communities of four species of ocean fish using 16S rRNA high-throughput sequencing to investigate the structural and functional features of these microbial communities across different fish species. By comparing the gut microbiota compositions of blue sharks (Prionace glauca), bigeye tuna (Thunnus obesus), sickle pomfret (Taractichthys steindachneri), and mackerel (Scomber japonicus), we identified several microbial taxa—including Photobacterium, Pelomonas, Ralstonia, and Rhodococcus—that were consistently detected across all samples, indicating they likely constitute a “common microbiota”. However, the relative abundances of these taxa varied significantly among species, with Photobacterium exhibiting the highest diversity. Blue sharks and bigeye tuna harbored relatively few dominant microbial species, but the abundance of these dominant bacteria was remarkably high, and inter-individual differences in microbial composition were pronounced. In contrast, mackerel and sickle pomfret contained a greater variety of dominant genera, each with low relative abundance, and inter-individual differences within the same species were minimal. Functionally, metabolic pathways, biosynthesis of secondary metabolites, and microbial metabolism represent the predominant functional categories of the intestinal microbiota in marine fish, with only minor interspecific differences observed. In contrast, biosynthesis of amino acids, ABC transporters, and two-component systems are the key functional pathways that exhibit significant variations across different fish species. Collectively, these findings reveal differences in gut microbial stability among different fish hosts. Such variations may be associated with the hosts’ energy utilization needs, and changes in the gut microbiota play a critical role in shaping the diverse survival strategies of these fish species. Full article

(This article belongs to the Section Biology and Ecology)

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14 pages, 297 KB

Open AccessArticle

Water Renewal Rate and Temperature on the Growth Performance and Physiology of Piaractus brachypomus in a Recirculating Aquaculture System (RAS)

by Pedro P. C. Pedras, Zandhor Lipovetsky, Fábio A. C. dos Santos, André de S. Souza, Luisa A. A. Silva, Gustavo S. da C. Júlio, Imaculada de M. C. Ananias, Sidney dos S. Silva, Ronald K. Luz and Gisele C. Favero

Fishes 2026, 11(1), 64; https://doi.org/10.3390/fishes11010064 - 19 Jan 2026

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Abstract

This study evaluated the effects of water renewal rate and temperature on the growth performance and physiological responses of juvenile Piaractus brachypomus reared in a recirculating aquaculture system (RAS). A total of 336 fish (1.35 ± 0.24 g) were distributed in six RAS [...] Read more.

This study evaluated the effects of water renewal rate and temperature on the growth performance and physiological responses of juvenile Piaractus brachypomus reared in a recirculating aquaculture system (RAS). A total of 336 fish (1.35 ± 0.24 g) were distributed in six RAS units under two water renewal rates (42 and 128 L h⁻¹) and three temperatures (26, 29, and 32 °C) for 45 days. Temperature was the main factor affecting growth, with higher final weight and total length at 29 and 32 °C throughout the experimental period. Water renewal rate significantly influenced feeding efficiency and energy allocation. Higher renewal (128 L h⁻¹) increased dissolved oxygen and daily feed intake and resulted in higher hemoglobin levels and hepatic lipid deposition, particularly at 32 °C, indicating greater metabolic activity. Conversely, the lower renewal rate (42 L h⁻¹) was associated with better feed conversion ratios at 29 °C and higher muscle lipid content at 26 °C, suggesting reduced energy expenditure. Hematocrit, total plasma protein, and cholesterol were primarily influenced by temperature, with higher values at 29 and 32 °C, while glucose, triglycerides, and liver enzymes were unaffected. Overall, temperatures of 29–32 °C optimized growth, while water renewal rate modulated feed utilization, physiological responses, and lipid deposition. These findings highlight the importance of jointly optimizing temperature and water renewal rate in RAS to enhance growth performance and metabolic balance in juvenile P. brachypomus. Full article

(This article belongs to the Special Issue Advances in the Physiology of Aquatic Organisms)

14 pages, 2042 KB

Open AccessArticle

Effects of Different Application Strategies of Copper-Loaded Montmorillonite on Growth, Intestinal Histology, and Rearing-Water Quality in Penaeus monodon

by Jieyi Wang, Yangyang Ding, Falin Zhou, Jianzhi Shi, Qibin Yang, Yundong Li, Jianhua Huang, Lishi Yang, Xueliang Sun and Song Jiang

Fishes 2026, 11(1), 63; https://doi.org/10.3390/fishes11010063 - 18 Jan 2026

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Abstract

Penaeus monodon is widely cultured in Asia; however, intensive farming practices often result in water-quality deterioration and compromised production performance. Copper-loaded montmorillonite (Cu-MMT) is a functional additive with adsorption and antimicrobial properties, yet the relative effectiveness of different application strategies remains insufficiently evaluated. [...] Read more.

Penaeus monodon is widely cultured in Asia; however, intensive farming practices often result in water-quality deterioration and compromised production performance. Copper-loaded montmorillonite (Cu-MMT) is a functional additive with adsorption and antimicrobial properties, yet the relative effectiveness of different application strategies remains insufficiently evaluated. In this study, 270 shrimp were assigned to three treatments: a control group (KZ), water application of Cu-MMT (PZ), and dietary inclusion of Cu-MMT (BZ). Juvenile Penaeus monodon with an initial body weight of 3.25 ± 0.15 g were used in the trial. Growth performance, intestinal histology, and rearing-water quality were assessed over a 56-day culture period. Shrimp in the BZ group exhibited a significantly higher weight gain rate (311.88 ± 38.17%) and survival rate (88.04%) than those in the KZ (247.45 ± 32.82%; 76.67%) and PZ (286.49 ± 29.78%; 83.33%) groups (p < 0.05). Intestinal histological observations revealed treatment-associated differences in morphology, with more pronounced intestinal enlargement observed in the PZ group, whereas the BZ group exhibited a more moderate intestinal architecture. Water-quality analyses showed that dietary Cu-MMT supplementation was associated with higher dissolved oxygen levels and lower concentrations of total ammonia nitrogen, sulfide, and dissolved iron, particularly during the later stages of the experiment. Overall, these results indicate that dietary inclusion of Cu-MMT provides more favorable outcomes than water application in improving growth performance and rearing-water quality in P. monodon culture under the experimental conditions tested. These findings highlight the importance of application strategy when evaluating functional additives in shrimp aquaculture. Full article

(This article belongs to the Special Issue Diet and Intestinal Microbiota of Fish)

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20 pages, 1461 KB

Open AccessArticle

Spatial and Economic Concentration of Offshore Mariculture in China: Insights from a Nation-Scale GIS Dataset

by Wei Yang, Yinping Hu and Kunlin Tang

Fishes 2026, 11(1), 62; https://doi.org/10.3390/fishes11010062 - 18 Jan 2026

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Abstract

China is the world’s leading producer of offshore mariculture, contributing more than 60 percent of global output. Yet the provincial distribution of mariculture space and its economic concentration are still not well described at a comparable national scale. This study draws on a [...] Read more.

China is the world’s leading producer of offshore mariculture, contributing more than 60 percent of global output. Yet the provincial distribution of mariculture space and its economic concentration are still not well described at a comparable national scale. This study draws on a publicly available nation-scale GIS dataset extracted from Landsat 8 imagery from 2018 to map offshore mariculture across nine coastal provinces and to quantify spatial inequality and specialization. The mapped offshore mariculture footprint totals 733,840 ha. The distribution is sharply uneven. Fujian alone reaches 183,025 ha, nearly thirty times the area of Hainan. The Gini coefficient is 0.412, and concentration ratios show that the top three provinces account for 64.0 percent of the total area, and the top five account for 84.5 percent. Location quotient results indicate strong specialization in Fujian, Jiangsu, and Hebei, while Hainan and Guangxi remain marginal. Cluster analysis further identifies three development modes: large-scale expansion, medium-scale and relatively balanced growth, and small-scale dispersed production. Overall, the pattern is consistent with resource endowment, agglomeration effects, and path dependence. The findings point to the need for improved coastal spatial planning, stronger interprovincial technology diffusion, and differentiated governance that balances efficiency with equity and environmental sustainability. Full article

(This article belongs to the Special Issue Advances in Fisheries Economics)

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18 pages, 1938 KB

Open AccessArticle

Reproductive Dynamics of the Blonde Ray (Raja brachyura) in Portuguese Waters: Timing, Maturity and Fecundity

by Catarina Maia, Ivone Figueiredo, Bárbara Serra-Pereira, Neide Lagarto, Inês Farias and Teresa Moura

Fishes 2026, 11(1), 61; https://doi.org/10.3390/fishes11010061 - 17 Jan 2026

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Abstract

Within the Rajidae family, the blonde ray (Raja brachyura) is considered one of the less resilient species to fishing pressure and other anthropogenic pressures, primarily due to its late maturity and large maximum size, which can exceed 120 cm total length. [...] Read more.

Within the Rajidae family, the blonde ray (Raja brachyura) is considered one of the less resilient species to fishing pressure and other anthropogenic pressures, primarily due to its late maturity and large maximum size, which can exceed 120 cm total length. This is the first study to provide comprehensive insights into the reproductive biology of Raja brachyura in the continental waters of Portugal, with insights into its timing, maturity, and fecundity. It was determined that egg-laying occurs from February to November, with a peak observed between April and September. Males were reproductively active throughout the year, with highest proportions of active males observed between January and May. The length at first maturity was estimated at 95.2 cm for females and 90.0 cm for males, corresponding to 85% of the maximum observed length in each sex. The potential fecundity was estimated at 115 follicles per female per year, and evidence suggests that the species has a determinate fecundity. The findings reinforce the appropriateness of current management measures in Portuguese continental waters, namely seasonal closure when overlapping with the peak of the reproductive season (May and June), and provide valuable scientific support for future conservation and management measures. Full article

(This article belongs to the Special Issue Ecology of Fish: Age, Growth, Reproduction and Feeding Habits)

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25 pages, 1443 KB

Open AccessReview

Microalgae as a Synergistic Enhancer for In Situ and Ex Situ Treatment Technologies in Sustainable Shrimp Aquaculture: A Critical Review

by Sheng Dong, Fei Huang, Xianghui Zou, Qiulan Luo and Jiancheng Li

Fishes 2026, 11(1), 60; https://doi.org/10.3390/fishes11010060 - 16 Jan 2026

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Abstract

The intensification of shrimp aquaculture is crucial for global food security, but poses significant environmental challenges. This review critically assesses the strengths and bottlenecks of two main treatment paradigms: in situ systems, chiefly biofloc technology (BFT), and advanced ex situ systems, such as [...] Read more.

The intensification of shrimp aquaculture is crucial for global food security, but poses significant environmental challenges. This review critically assesses the strengths and bottlenecks of two main treatment paradigms: in situ systems, chiefly biofloc technology (BFT), and advanced ex situ systems, such as recirculating aquaculture systems (RASs), constructed wetlands (CWs), and membrane bioreactors (MBRs). Although BFT enables nutrient recycling, it suffers from nitrate accumulation and a high energy demand. Likewise, ex situ technologies can achieve a high treatment efficiency, but contend with high costs, large footprints, or membrane fouling. In this review, we propose the strategic integration of microalgae, representing a universal and synergistic solution for overcoming these disparate bottlenecks. We dissect how a microalgal co-culture can simultaneously remove nitrate and reduce the aeration costs in BFT systems. Furthermore, we explore how microalgae-based units can serve as efficient polishing steps for RASs, enhance the performance of CWs, and mitigate fouling in MBRs. This review delves into the fundamental mechanisms of the microalgal–bacterial symbiosis that underpins these enhancements. Finally, we highlight the valorization of the resulting algal biomass as a high-value aquafeed ingredient, which can transform waste management into a value-creation opportunity. This review aims to provide a comprehensive roadmap for developing next-generation, microalgae-enhanced aquaculture systems. Full article

(This article belongs to the Special Issue Advances in the Application of Microalgae in Aquaculture)

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20 pages, 3926 KB

Open AccessArticle

Hydrodynamic Performance of Cubic Artificial Reefs During Deployment Process Based on Smoothed Particle Hydrodynamics

by Wenhua Chu, Shijing Lu, Zijing Zhao, Xinyang Zhang and Yulei Huang

Fishes 2026, 11(1), 59; https://doi.org/10.3390/fishes11010059 - 16 Jan 2026

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Abstract

Currently, research on the hydrodynamic characteristics of artificial reef deployment still faces challenges such as insufficient environmental coupling, but accurate simulation of the deployment process holds significant engineering importance for optimizing deployment efficiency and ensuring reef stability. This study employs the Smoothed Particle [...] Read more.

Currently, research on the hydrodynamic characteristics of artificial reef deployment still faces challenges such as insufficient environmental coupling, but accurate simulation of the deployment process holds significant engineering importance for optimizing deployment efficiency and ensuring reef stability. This study employs the Smoothed Particle Hydrodynamics (SPH) method to establish a 3D numerical model, focusing on the influence of key parameters—inflow velocity and water entry angle—on the hydrodynamic characteristics of cubic artificial reef deployment. The results indicate that under flow velocities of 0.4–0.5 m/s, pressure fluctuations are relatively minor, with peak pressure gradients below 15 kPa/m, exhibiting a gradual trend, while particle concentration remains high, and drag gradually increases. At flow velocities of 0.6–0.8 m/s, the maximum pressure at the bottom reaches up to 35 kPa, with low-pressure areas at the tail dropping to −10 kPa; particle concentration decreases compared to conditions at 0.4–0.5 m/s; settling time extends from 8.4 s to 12 s, representing a 42% increase. Under different water entry angles, drag varies nonlinearly with the angle, reaching its maximum at 20° and its minimum at 25°, with a reduction of approximately 47% compared to the maximum. The anti-sliding safety factor and anti-overturning safety factor are used to assess the stability of the cubic reef placed on the seabed. Across different inflow velocities, the anti-sliding safety factor of the cubic artificial reef significantly exceeds 1.2, whereas the anti-overturning safety factor is below 1.2 at 0.4 m/s but exceeds 1.2 at velocities of 0.5 m/s and above, indicating that the reef maintains stability under the majority of these flow conditions. Our findings provide a scientific basis for the deployment process, site selection, and geometric design of cubic artificial reefs, offering valuable insights for the precise deployment and structural optimization of artificial reefs in marine ranching construction. Full article

(This article belongs to the Special Issue Engineering Solutions for Sustainable Offshore Aquaculture and Fisheries)

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31 pages, 3950 KB

Open AccessArticle

Effects of Red Kojic Rice Supplementation on Growth, Immunity, Antioxidant Capacity, and Intestinal Health of Litopenaeus vannamei Fed a Diet with Fish Meal Replacement by Soybean Meal

by Qianping Huang, Hongkai Ye, Zhanzhan Wang, Bo Liu, Min Yang, Xiaobin Chen, Shengli Liu and Chuanpeng Zhou

Fishes 2026, 11(1), 58; https://doi.org/10.3390/fishes11010058 - 16 Jan 2026

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Abstract

This study aimed to investigate the effects of adding Red kojic rice (RKR) on the growth performance, digestive enzyme activity, non-specific immunity, antioxidant capacity, and intestinal health of Litopenaeus vannamei fed a diet with fishmeal replacement by soybean meal. Shrimps (initial mean weight [...] Read more.

This study aimed to investigate the effects of adding Red kojic rice (RKR) on the growth performance, digestive enzyme activity, non-specific immunity, antioxidant capacity, and intestinal health of Litopenaeus vannamei fed a diet with fishmeal replacement by soybean meal. Shrimps (initial mean weight = 1.88 ± 0.03 g) were fed six experimental diets for 8 weeks, including a normal fishmeal control group (FM), a soybean meal-replaced fishmeal group (H0), and four soybean meal-replaced fishmeal groups supplemented with 0.5%, 1%, 2%, and 4% RKR, respectively, which are designated as H1, H2, H3, and H4, respectively. Each group had three replicates, with 30 shrimp per replicate. The results showed that the final average weight (FWG), weight gain rate (WG), and specific growth rate (SGR) of H2 group were significantly higher than those of H0, H3, and H4 groups (p < 0.05). The feed conversion ratio (FCR) of H2 group was significantly lower than that of H0 and H4 groups (p < 0.05). In contrast to the H0 group, the blood ACP activity in the H2 group was significantly increased (p < 0.05). The blood lysozyme (LYZ) activity in H3 group was significantly higher than that in H1 group (p < 0.05), while the opposite was true for phenoloxidase (PO). The activities of trypsin and amylase in hepatopancreas of H3 group were significantly higher than those of H0 and H1 groups (p < 0.05). Compared with the FM group, the hepatopancreatic malondialdehyde (MDA) levels in H0, H3, and H4 groups were significantly increased (p < 0.05). Compared with the H0 group, the hepatopancreatic MDA levels in H1 and H2 groups were significantly decreased (p < 0.05). Analysis of gene expression levels in hepatopancreas revealed that antioxidant (gpx, sod, cat, gst, nrf2, trx, and ho-1), non-specific immune (tnf-α, il-1β, and ifn-γ), and digestive (trypsin and α-amylase) genes were suppressed in the H0 group but enhanced by RKR supplementation. Similar expression patterns of those genes were observed in the intestine. Microbial community analysis showed reduced diversity and altered composition in the H0 group, which were partially restored by RKR. Network analysis showed “small-world” property in microbial co-occurrence network. Metabolomic analysis revealed that among the differential metabolites, Bismurrayaquinone A and Harmol exhibit highly significant differences. Correlation analysis revealed that beneficial bacteria Rhodococcus_C and Oceanobacillus in H2 group exhibited higher richness and showed significant correlation. In conclusion, supplementation of 0.5–2% RKR promoted the growth performance, digestive enzyme activity, non-specific immunity, antioxidant capacity, and intestinal health of shrimp fed a diet with fishmeal replacement by soybean meal. The optimal RKR supplementing content is 1%. Full article

(This article belongs to the Section Nutrition and Feeding)

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16 pages, 7656 KB

Open AccessArticle

Transcriptome Sequencing Reveals Dynamic Gene-Expression Profiles During Early Embryonic Development of Sichuan Taimen (Hucho bleekeri)

by Yeyu Chen, Zhao Liu, Huanchao Yang, Qinyao Wei, Yanling Chen, Guiliang Liu, Wei Jin and Hua Li

Fishes 2026, 11(1), 57; https://doi.org/10.3390/fishes11010057 - 16 Jan 2026

Viewed by 192

Abstract

The Sichuan taimen (Hucho bleekeri) is a flagship species for the Yangtze River and is classified as critically endangered by the IUCN. Successful artificial breeding and conservation efforts are therefore essential for maintaining population stability. The early embryonic stage is the [...] Read more.

The Sichuan taimen (Hucho bleekeri) is a flagship species for the Yangtze River and is classified as critically endangered by the IUCN. Successful artificial breeding and conservation efforts are therefore essential for maintaining population stability. The early embryonic stage is the foundation of the entire life cycle and is critical for subsequent survival and growth. Here, we aimed to investigate gene-expression profiles across eight developmental stages through RNA-seq sequencing: fertilized egg, embryonic shield elevation, cleavage, blastula, gastrula, neurula, brain differentiation, and hatching. Time-series analysis revealed remarkable gene-expression changes between the cleavage and embryonic shield elevation, gastrula and blastula, and brain differentiation and hatching stages. The expression levels of cell cycle-related genes—including ccn2d, ccna2, cdk11, cdk17, cdka2, cdkl3, plk1, and others—decreased during embryonic development. Genes associated with muscle development, such as myl9, mylk, and tnnc2, were present in all stages and significantly enriched at hatching, while others were nearly absent during early development. In metabolic pathways, genes related to lipid metabolism and glycolysis were significantly expressed in the hatching stage. Regarding immune-related genes, complement genes were notably enriched at hatching, whereas cfh and cfb were expressed throughout development. Genes involved in adaptive immunity, such as mhc I, mhc II, tcr, and T-cell marker genes, were either not expressed or only weakly expressed in all stages. The results can provide insights into regulatory mechanisms underlying early embryonic development in fishes and provide general knowledge about salmonid development. Full article

(This article belongs to the Special Issue Freshwater Fishes: Taxonomic Diversity, Conservation Concerns, and Future Directions)

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11 pages, 1527 KB

Open AccessCommunication

Comparative Transcriptome Analysis of White and Orange Skin of Clownfish Identifying Differentially Expressed Genes (DEGs) Underlying Pigment Expression

by Heegun Lee, Taehyug Jeong, Yeongkuk Kim, Sumi Jung, Jiyong Choi, Min-min Jung, Seunghwan Ko, Hayeong Oh, Juhyeok Kim, Jehee Lee and Seung Hwan Lee

Fishes 2026, 11(1), 56; https://doi.org/10.3390/fishes11010056 - 16 Jan 2026

Viewed by 290

Abstract

Although the clownfish, Amphiprion ocellaris (A. ocellaris), is a popular ornamental marine fish worldwide, the mechanisms underlying color pattern variation remain unclear. Given that the Platinum-type clownfish, nearly entirely white, has high economic value, understanding the biological mechanism that accounts for the [...] Read more.

Although the clownfish, Amphiprion ocellaris (A. ocellaris), is a popular ornamental marine fish worldwide, the mechanisms underlying color pattern variation remain unclear. Given that the Platinum-type clownfish, nearly entirely white, has high economic value, understanding the biological mechanism that accounts for the difference between orange and white colors in A. ocellaris is crucial. To investigate these coloration differences, we performed RNA sequencing analysis and identified differentially expressed genes (DEGs) by comparing white and orange skin samples from three A. ocellaris individuals. A total of 76 DEGs were detected, including 56 downregulated and 20 upregulated genes. DEG sequences were annotated using Danio rerio and Stegastus partitus as reference species, selecting the best hit based on the lowest E-value. A protein–protein interaction (PPI) network and Gene Ontology biological process terms were additionally analyzed. Several DEGs previously reported to be associated with pigmentation, including hpdb, cldn11b, sfrp5, slc2a9, slc2a11b, si:ch211-256m1.8, fhl2, rab38, and ttc39b were identified. Based on the functions of these DEGs, it is inferred that leucophores and xanthophores contribute to both white and orange coloration by modulating related genes, including slc2a11b and slc2a9. Additionally, sfrp5, sost, and sp7 genes were identified to interact with each other in the PPI analysis, with sfrp5 and sost being associated with the Wnt signaling pathway, which contributes to melanocyte specification and osteoblast differentiation. Based on these findings, we propose sost and sp7 as candidate genes that might provide insights relevant to extreme white pigmentation phenotypes, such as those observed in Platinum-type clownfish. For a clearer understanding, further studies integrating quantitative genetics and functional analyses are required. Full article

(This article belongs to the Section Genetics and Biotechnology)

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16 pages, 1006 KB

Open AccessArticle

Habitat-Selecting Life History

by Douglas W. Morris and Per Lundberg

Fishes 2026, 11(1), 55; https://doi.org/10.3390/fishes11010055 - 15 Jan 2026

Viewed by 162

Abstract

Adaptive life histories emerge through their environmentally dependent effects on fitness. Those effects are consequences of habitat quality and the density-dependent decisions that organisms make on habitat choice. Density dependence for ideal organisms maximizing fitness through habitat selection is uniquely revealed by their [...] Read more.

Adaptive life histories emerge through their environmentally dependent effects on fitness. Those effects are consequences of habitat quality and the density-dependent decisions that organisms make on habitat choice. Density dependence for ideal organisms maximizing fitness through habitat selection is uniquely revealed by their habitat isodars, lines in the state space of species’ densities that confer equal fitness between habitats coupled by dispersal. We use isodars to structure simple simulations of habitat selection in stable and stochastic environments. The simulations demonstrate an indirect effect of ideal habitat selection that can dampen otherwise wide fluctuations in abundance and their impact on pace-of-life strategies. The ability of habitat selection to equalize fitness between habitats also has a direct effect on life history evolution. Habitat selection can promote phenotypically plastic life histories between habitats that might otherwise convey divergent genetically fixed strategies. The direct and indirect effects on life history demonstrate that it is not just habitat that requires our concern in managing and conserving nature, but how those activities are likely to impinge on habitat selection. Full article

(This article belongs to the Special Issue Habitat as a Template for Life Histories of Fish)

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20 pages, 1997 KB

Open AccessArticle

Effects of Four Light Colors on Physiology, Antioxidant Enzyme Activity, Shell Pigmentation, and Genes Associated with Body Color Formation in Procambarus clarkii

by Zhuozhuo Ai, Zhigang Yang, Jianhua Ming, Lu Zhang, Xiaoru Chen, Zhiqiang Xu, Wuxiao Zhang, Aiming Wang, Hongyan Tian, Silei Xia and Aqin Chen

Fishes 2026, 11(1), 54; https://doi.org/10.3390/fishes11010054 - 15 Jan 2026

Viewed by 316

Abstract

Light plays a critical role in the physiology and pigmentation of aquatic animals. Regulating the light environment of aquatic animals offers insights into healthy aquaculture practices. In this study, Procambarus clarkii were reared under four different light colors—white (WL), red (RL), blue (BL), [...] Read more.

Light plays a critical role in the physiology and pigmentation of aquatic animals. Regulating the light environment of aquatic animals offers insights into healthy aquaculture practices. In this study, Procambarus clarkii were reared under four different light colors—white (WL), red (RL), blue (BL), and green (GL)—for 21 days, with four replicates per light color. Morphological characteristics did not differ among light treatments. However, significant differences were observed in hemolymph cortisol levels and tyrosinase activity across different tissues (hemolymph, muscle, hepatopancreas) among groups (RL > BL > GL > WL). Hepatopancreatic CAT activity in WL was significantly higher than that in GL and BL, whereas hepatopancreatic MDA content was highest in BL. Regarding chromatic parameters, the yellow color of the RL cephalothorax cuticle and the red color of the muscle were more pronounced than in WL, The chela cuticle of GL is darker than RL, while the red color of the chela cuticle was more pronounced than in WL.. For pigment content, cephalothorax cuticle astaxanthin content in BL was significantly higher than that in other light color groups, while abdominal cuticle astaxanthin content was lowest in BL. Chela cuticle astaxanthin content in RL was significantly higher than that in WL, and chela cuticle astaxanthin and lutein contents in WL were significantly lower than those in BL and GL. Compared with WL, hepatopancreatic glutathione S-transferase P1 (GSTP1) mRNA expression significantly decreased under colored light, whereas NinaB mRNA expression significantly increased under RL and BL. These results indicate that light color does not affect the morphological characteristics of P. clarkii but significantly modulates oxidative stress responses, physiological status and energy metabolism. Different light colors may mediate carotenoid transport and deposition by regulating the expression of GSTP1, NinaB, leading to specific chromatic differences in different body parts of P. clarkii. Comprehensive analysis revealed that the red light environment exerted a more positive effect on enhancing the body color of P. clarkii. This study provides a reference for revealing the mechanism of light color regulating crustacean physiological function and pigmentation and optimizing aquaculture model. Full article

(This article belongs to the Section Aquatic Invertebrates)

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15 pages, 2108 KB

Open AccessArticle

Age Structure, Growth Parameters, and Otolith Traits of Two Species of the Genus Trachurus in the Central Mediterranean

by Vasiliki Nikiforidou, Chryssi Mytilineou, Vasileios Xenikakis and Aikaterini Anastasopoulou

Fishes 2026, 11(1), 53; https://doi.org/10.3390/fishes11010053 - 15 Jan 2026

Viewed by 253

Abstract

The Atlantic horse mackerel (Trachurus trachurus) and the Mediterranean horse mackerel (T. mediterraneus) are two commercially important species whose biological traits remain insufficiently studied in the Central Mediterranean Sea. This study examines their age, growth pattern, and, for the [...] Read more.

The Atlantic horse mackerel (Trachurus trachurus) and the Mediterranean horse mackerel (T. mediterraneus) are two commercially important species whose biological traits remain insufficiently studied in the Central Mediterranean Sea. This study examines their age, growth pattern, and, for the first time, otolith morphology in both species in the Eastern Ionian Sea. The intercept of the weight–length relationship was a = 0.00599 (95% CI = 0.0050–0.0072) for T. trachurus and a = 0.00801 (95% CI = 0.0072–0.0089) for T. mediterraneus, and the slope was b = 3.121 (95% CI: 3.058–3.183) and b = 2.994 (95% CI: 2.957–3.031), respectively. Age was estimated by counting annual growth increments, visible as alternating opaque and clear bands along the axis of the left sagittal otolith from the core to the posterior margin. Von Bertalanffy growth parameters were estimated as L_∞ = 34.65 cm, k = 0.31 year⁻¹, and t₀= −1.11 years for T. trachurus and L_∞ = 35.98 cm, k = 0.23 year⁻¹, and t_o = −1.60 years for T. mediterraneus. Otolith morphometrics showed significantly higher values (ANOVA, p-value < 0.05) in T. mediterraneus for all morphometric variables, except one, indicating larger and wider otoliths than those of T. trachurus, which can be a tool to distinguish the two species. A strong correlation was observed between the total length of the body and otolith metrics in both species. This study enhanced our scientific knowledge on the studied species’ life history traits and provides information for further ecological and stock assessment studies. Full article

(This article belongs to the Special Issue Age Determination of Aquatic Animals)

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18 pages, 2825 KB

Open AccessArticle

Expression Profiles of Growth-Related Genes in CRISPR/Cas9-Mediated MRF4-Crispant Nile Tilapia

by Zahid Parvez Sukhan, Yusin Cho, Doohyun Cho, Cheol Young Choi and Kang Hee Kho

Fishes 2026, 11(1), 52; https://doi.org/10.3390/fishes11010052 - 14 Jan 2026

Viewed by 209

Abstract

Genome editing of late myogenic regulators provides a way to dissect the mechanisms through which transcriptional programs and growth-related signaling pathways shape muscle gene expression programs in farmed fish. This study disrupted myogenic regulatory factor 4 (MRF4) in Nile tilapia using [...] Read more.

Genome editing of late myogenic regulators provides a way to dissect the mechanisms through which transcriptional programs and growth-related signaling pathways shape muscle gene expression programs in farmed fish. This study disrupted myogenic regulatory factor 4 (MRF4) in Nile tilapia using CRISPR/Cas9 to examine downstream transcriptional changes in fast skeletal muscle across the trunk, belly, and head regions. Adult F0 crispants carried a frameshift mutation that truncated the basic helix–loop–helix domain and showed an approximate 80–85% reduction in MRF4 mRNA across the trunk, belly, and head muscles. The expression of 23 genes representing myogenic regulatory factors, MEF2 paralogs, structural and contractile components, non-myotomal regulators, cell adhesion and fusion-related transcripts, and growth-related genes within the GH–IGF–MSTN axis was quantified and compared between wild-type and MRF4-crispants. Expressions of major structural genes remained unchanged despite MRF4 depletion, whereas MyoG and MyoD were upregulated together with MEF2B and MEF2D, indicating strong transcriptional compensation. Twist1, ID1, PLAU, CDH15, CHRNG, NCAM1, MYMK, GHR, and FGF6 were also significantly elevated, while IGF1 was reduced, and MSTN remained stable. Together, these results show that MRF4 loss is associated with coordinated transcriptional changes in regulatory and growth-related pathways, while major fast-muscle structural and contractile transcript levels remain stable, thereby highlighting candidate transcriptional targets for future studies that will evaluate links to muscle phenotype and growth performance in Nile tilapia. Full article

(This article belongs to the Special Issue Genetics and Breeding of Fishes)

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15 pages, 3522 KB

Open AccessArticle

Combined Microplastics and Cadmium Exposure Induces Persistent Gut Microbiota Dysbiosis in Pearl Oyster Pinctada fucata martensii

by Luomin Huang, Yujing Lin, Lintao Liu, Qin Su, Jiaen Liu, Chuangye Yang, Jiaying Yao, Zixin Gao and Yuewen Deng

Fishes 2026, 11(1), 51; https://doi.org/10.3390/fishes11010051 - 14 Jan 2026

Viewed by 188

Abstract

In marine aquaculture environments, microplastics (MPs) and cadmium (Cd) are widespread contaminants that may jointly affect host–microbe interactions. Here, we examined the combined effects of MPs (5 mg/L) and Cd (5 μg/L) on the intestinal microbial community of pearl oysters after a 48 [...] Read more.

In marine aquaculture environments, microplastics (MPs) and cadmium (Cd) are widespread contaminants that may jointly affect host–microbe interactions. Here, we examined the combined effects of MPs (5 mg/L) and Cd (5 μg/L) on the intestinal microbial community of pearl oysters after a 48 h exposure, followed by a 5-day recovery period. Gut microbiota dynamics were characterized using 16S rRNA gene sequencing. Alpha diversity did not vary significantly, whereas beta diversity showed marked alterations in community composition among the different exposure treatments. LEfSe analysis revealed distinct microbial biomarkers and putative pathogens under each treatment: Sulfitobacter in the MPs-alone group; Vibrio and Candidatus_Megaira in the Cd-alone group; and Tenacibaculum, Roseibacillus, and Enterovibrio across different co-exposure and recovery groups. A brief recovery period partially decreased the abundance of certain pathogens (e.g., Vibrio), yet some taxa (e.g., Enterovibrio and Tenacibaculum) remained enriched. These results indicate that exposure to MPs and Cd, whether alone or in combination, disrupts gut microbial homeostasis in pearl oysters by reshaping community structure and promoting the proliferation of potential pathogens, with some disturbances persisting after exposure ceases. Generally, our findings will aid evaluation of the ecological risks of combined pollutants in marine aquaculture systems. Full article

(This article belongs to the Special Issue Biology and Culture of Marine Invertebrates)

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18 pages, 2041 KB

Open AccessArticle

Seasonal and Size-Related Variation in Diet Composition and Feeding Strategies of the Robustus Tonguefish, Cynoglossus robustus in the Yeosu Coast, Korea

by Seung Jo Han and Seong Yong Moon

Fishes 2026, 11(1), 50; https://doi.org/10.3390/fishes11010050 - 14 Jan 2026

Viewed by 215

Abstract

This study examined the seasonal and size-related variations in the diet composition and feeding strategies of the robust tonguefish Cynoglossus robustus collected in the Yeosu Coast, Korea, from January to December 2024. Stomach content analysis identified amphipods, polychaetes, and brachyurans as the dominant [...] Read more.

This study examined the seasonal and size-related variations in the diet composition and feeding strategies of the robust tonguefish Cynoglossus robustus collected in the Yeosu Coast, Korea, from January to December 2024. Stomach content analysis identified amphipods, polychaetes, and brachyurans as the dominant prey items. Ontogenetic dietary shifts were evident, with individuals < 25 cm TL feeding mainly on amphipods, whereas larger individuals consumed more polychaetes and brachyurans, indicating a shift toward larger and more energy-efficient prey with growth. Amphipods, with Ampelisca sp. being predominant, were predominant in spring and summer, whereas crabs and polychaetes increased in autumn and winter, respectively. Seasonal variation was attributed to environmental factors and post-spawning feeding recovery. The estimated trophic level (3.22) suggests that C. robustus functions as a mesopredator consuming benthic invertebrates and plays an essential role in energy transfer within the coastal benthic ecosystem. These findings provide fundamental ecological insights into the trophic structure of the coastal ecosystem in the southern sea of Korea and serve as a scientific basis for sustainable fisheries resource management. Full article

(This article belongs to the Special Issue Ecology of Fish: Age, Growth, Reproduction and Feeding Habits)

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13 pages, 2002 KB

Open AccessArticle

Transition to Time-Dependent Artificial Feed Induces Histological and Apoptotic Alterations in Mandarin Fish (Siniperca chuatsi)

by Zhou Zhang, Qi Deng, Zhonggui Xie, Min Xie and Shaoming Li

Fishes 2026, 11(1), 49; https://doi.org/10.3390/fishes11010049 - 13 Jan 2026

Viewed by 128

Abstract

This study aimed to investigate the response mechanisms of liver and gill tissues in mandarin fish (Siniperca chuatsi) at the histological, apoptotic, and gene expression levels during the weaning process from live prey to artificial feed. By analyzing fish samples at [...] Read more.

This study aimed to investigate the response mechanisms of liver and gill tissues in mandarin fish (Siniperca chuatsi) at the histological, apoptotic, and gene expression levels during the weaning process from live prey to artificial feed. By analyzing fish samples at different domestication stages (D0, D7, D14), the results revealed that: (1) Histologically, the gill filaments exhibited shortening and thickening post-domestication, while the liver showed increased vacuolation; (2) apoptosis detection (TUNEL assay) and analysis of apoptosis-related gene (Bax/Bcl-2) expression indicated that the gill tissue experienced a significant increase in apoptosis at the mid-domestication stage (D7), which returned to baseline levels later (D14), whereas hepatic apoptosis showed no significant changes throughout the process; (3) transcriptome sequencing identified 3405 and 881 differentially expressed genes (DEGs) in the liver and gill tissues, respectively, and the significantly enriched pathways were steroid biosynthesis in the liver and alanine, aspartate, and glutamate metabolism in the gills. The apoptosis pathway was also significantly enriched in both tissues. GO analysis further indicated that the DEGs were primarily associated with metabolic processes, oxidative stress, and cell apoptosis. In conclusion, artificial feed domestication induces adaptive changes in the tissue structure and molecular profiles of the gill and liver in mandarin fish. The gill response to dietary transition is more rapid and characterized by a reversible apoptotic process, providing a theoretical foundation for understanding the stress mechanisms associated with domestication and promoting healthy aquaculture practices for this species. Full article

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12 pages, 1633 KB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of TTC39 Genes Associated with Red Skin Coloration in Plectropomus leopardus

by Yang Li, Xin Zhang, Xiaojing Wu, Yafeng Tan, Nana Lu, Zhenlong Jiang, Jin Gao, Jian Luo and Xin Wen

Fishes 2026, 11(1), 48; https://doi.org/10.3390/fishes11010048 - 12 Jan 2026

Viewed by 325

Abstract

Despite the recognized involvement of TTC39 family genes in metabolism related to pigment deposition, their evolutionary features and potential roles in body coloration in teleost fish remain largely unexplored. We identified three TTC39 genes in Plectropomus leopardus, conserved domains, and evolutionary relationships. [...] Read more.

Despite the recognized involvement of TTC39 family genes in metabolism related to pigment deposition, their evolutionary features and potential roles in body coloration in teleost fish remain largely unexplored. We identified three TTC39 genes in Plectropomus leopardus, conserved domains, and evolutionary relationships. The three genes (TTC39A, TTC39B, and TTC39C) were mapped to different chromosomes, yet they shared similar conserved protein domains. Phylogenetic and collinearity analyses indicated that TTC39 genes are evolutionarily conserved among Danio rerio. Gene structure and motif analyses further highlighted the homology and distributional diversity within the TTC39 family. Quantitative expression assays comparing red and black skin revealed significant upregulation of TTC39A and TTC39B in red skin, suggesting that these genes play a role in regulating skin color. These findings provide a foundation for future studies examining how TTC39 genes regulate red skin coloration in P. leopardus. Full article

(This article belongs to the Section Genetics and Biotechnology)

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21 pages, 7183 KB

Open AccessArticle

From Biofouling to Crop Resource: Novel Opportunities as Extractive Species in a Mediterranean IMTA Pilot

by Daniele Arduini, Silvia Fraissinet, Sergio Rossi, Claudio Calabrese, Lorenzo Doria and Adriana Giangrande

Fishes 2026, 11(1), 47; https://doi.org/10.3390/fishes11010047 - 12 Jan 2026

Viewed by 327

Abstract

Biofouling communities are usually managed as pests in aquaculture, yet their natural proliferation in fish farms makes them also promising IMTA extractive components. The growth and biomass production of four dominant macrofoulers, Mytilus galloprovincialis (mussels), Sabella spallanzanii (polychaete worms), Phallusia mammillata and Styela [...] Read more.

Biofouling communities are usually managed as pests in aquaculture, yet their natural proliferation in fish farms makes them also promising IMTA extractive components. The growth and biomass production of four dominant macrofoulers, Mytilus galloprovincialis (mussels), Sabella spallanzanii (polychaete worms), Phallusia mammillata and Styela plicata (ascidians), were evaluated under a novel IMTA system in the Ionian Sea (southern Italy). Coconut-fiber ropes (10 m) were deployed around fish cages in October 2022 and monitored over a 1-year cycle. Monthly density, length-frequency and cohort analyses combined with species-specific length-weight relationships were used to estimate target species’ growth and biomass. Mytilus and Sabella showed single-cohort dynamics, with densities steadily declining over time, whereas ascidians displayed continuous recruitment allowing for additional rope-deployment windows. Specific growth rates in length were significantly higher in Phallusia and Sabella (≈25% month⁻¹) than in Mytilus and Styela (≈17 and 22% month⁻¹). Total macrofouling biomass (live weight) increased from ≈350 kg in May to a peak of ≈2500 kg in August, remaining as high in October. Mytilus and Sabella accounted for 60–80% of total biomass while ascidians contributed 20–40%. Beyond environmental restoration, this multispecies biomass offers several potential commercial opportunities and could be further valorized through biorefinery-based cascading extraction, including final conversion into bioenergy. Overall, IMTA could leverage traditionally undesired fouling organisms as multifunctional crops, enhancing bioremediation while supporting circular blue-bioeconomy principles. Future research should focus on optimizing rope deployment timing, harvesting strategies, and biomass valorization pathways to fully exploit the emerging potential of integrating multispecies fouling biomass within IMTA systems. Full article

(This article belongs to the Special Issue Integrated Multi-Trophic Aquaculture (IMTA))

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20 pages, 3883 KB

Open AccessArticle

Physiological Responses of Kalibaus (Labeo calbasu) to Temperature Changes: Metabolic, Haemato-Biochemical, Hormonal and Immune Effects

by Masuda Sultana Mimi, Simon Kumar Das, Mohammad Lutfar Rahman, Mohammad Abdus Salam, Md. Nushur Islam, Tamanna Rahman, Sumi Rani Das, Mohammad Nazmol Hasan and Sabuj Kanti Mazumder

Fishes 2026, 11(1), 46; https://doi.org/10.3390/fishes11010046 - 10 Jan 2026

Viewed by 340

Abstract

A global interest in the cultivation of Kalibaus (Labeo calbasu) has emerged due to decreasing natural stocks and a consistent rise in market value and demand. Given these concerns, understanding the species’ physiological responses to environmental changes is crucial. The present [...] Read more.

A global interest in the cultivation of Kalibaus (Labeo calbasu) has emerged due to decreasing natural stocks and a consistent rise in market value and demand. Given these concerns, understanding the species’ physiological responses to environmental changes is crucial. The present research aimed to assess the effect of varying environmental temperatures on metabolism, haemato-biochemical indices, hormonal concentrations and immune responses in L. calbasu. This study was conducted in triplicate using 100 L glass aquariums at four different temperatures: 22, 26, 30, and 34 °C. The highest weight and length gain were observed at 30 °C, while the lowest occurred at 22 °C. Notably, the best feed conversion ratio (FCR) of 1.51 ± 0.03 was also recorded at 30 °C. Although haematological and biochemical parameters remained within normal ranges, they varied with temperature changes. Indicators of cold and heat stress were evident through lower hematocrit levels and higher white blood cell (WBC) counts. Biochemical indicators such as serum albumin (1.84 ± 0.05 g dL⁻¹), serum globulin (1.64 ± 0.06 gdL⁻¹), HCO₃ (30.93 ± 0.62), Na⁺ (115.60 ± 3.72 mmolL⁻¹), alkaline phosphatase (93.33 ± 9.39 AP, IUL⁻¹), and AST/SGOT (21.00 ± 4.55 UL⁻¹) were significantly higher at 30 °C. Regarding hormonal responses, peak levels of growth hormone (GH), triiodothyronine (T3) (1.44 ± 0.07 ngmL⁻¹), and thyroxine (T4) were recorded at 30 °C. Meanwhile, serum cortisol (1.62 ± 0.06 µgdL⁻¹) and adrenocorticotropic hormone (ACTH) (18.01 ± 3.26 pgmL⁻¹) were highest at 34 °C. Immune responses were strongest between 26 and 30 °C. In conclusion, the results suggest that L. calbasu should ideally be cultured between 26 and 30 °C for optimum growth and health, making it ideal for commercial farming. Full article

(This article belongs to the Special Issue Advancing Fish Nutrition Research for Sustainable Aquaculture)

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18 pages, 4041 KB

Open AccessArticle

Nesting and Reproductive Behavior of the Sand-Dwelling Goby Hazeus ammophilus (Gobiidae) with Radial Ditches Around Its Nest

by Hiroshi Kawase and Takeru Tsuhako

Fishes 2026, 11(1), 45; https://doi.org/10.3390/fishes11010045 - 9 Jan 2026

Viewed by 543

Abstract

The reproductive behavior and nest-building activity of the sand-dwelling goby Hazeus ammophilus were investigated to examine its nesting characteristics and to determine how and why this species builds radial structures around its nests. Field observations revealed that males spawned with multiple females in [...] Read more.

The reproductive behavior and nest-building activity of the sand-dwelling goby Hazeus ammophilus were investigated to examine its nesting characteristics and to determine how and why this species builds radial structures around its nests. Field observations revealed that males spawned with multiple females in open muddy-sand bottoms, using bivalve shells or fallen leaves as spawning substrates. Males cared for eggs after spawning and repeatedly mated with multiple females, suggesting a male-territory-visiting polygamous mating system. A distinctive feature of this species was the presence of radial ditches extending from the nest. These ditches developed through repeated male behaviors of digging from the nest toward the surrounding area and sweeping accumulated sand out of the nest, resulting in a crater-like structure around the nest. These behaviors may contribute to cleaning and stabilizing the spawning substrate, and the resulting structures themselves may also be involved in female mate choice. Taken together, these findings indicate that H. ammophilus has evolved a flexible reproductive strategy, and nest-building behavior possibly adapted to unstable open sandy environments, highlighting the behavioral diversity and ecological plasticity within gobiid fishes. Full article

(This article belongs to the Section Biology and Ecology)

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4 pages, 147 KB

Open AccessEditorial

Advances in Aquaculture Feed Additives: Insights from the Special Issue

by Adolfo Jatobá and Delano Dias Schleder

Fishes 2026, 11(1), 44; https://doi.org/10.3390/fishes11010044 - 9 Jan 2026

Viewed by 246

Abstract

Aquaculture continues to expand globally and is now responsible for providing more than half of the aquatic products consumed worldwide [...] Full article

(This article belongs to the Special Issue Advances in Aquaculture Feed Additives)

20 pages, 3383 KB

Open AccessArticle

Gonadal Transcriptome Analysis Identifies Sex-Related Genes and Regulatory Pathways in Spotted Longbarbel Catfish (Hemibagrus guttatus)

by Kun Zhao, Yuanyuan Wang, Yexin Yang, Yi Liu, Chao Liu, Shandian Zhu, Jinhui Sun and Xidong Mu

Fishes 2026, 11(1), 43; https://doi.org/10.3390/fishes11010043 - 9 Jan 2026

Viewed by 371

Abstract

Hemibagrus guttatus is a large omnivorous fish of significant economic value, listed as a Class II protected species in the National Key Protected Wildlife List in 2021 in China. To provide a theoretical foundation for the artificial breeding of H. guttatus, this [...] Read more.

Hemibagrus guttatus is a large omnivorous fish of significant economic value, listed as a Class II protected species in the National Key Protected Wildlife List in 2021 in China. To provide a theoretical foundation for the artificial breeding of H. guttatus, this study employs high-throughput transcriptome sequencing of testes and ovaries to elucidate the molecular regulatory pathways involved in sex differentiation. Because H. guttatus exhibits no obvious sexual dimorphism even during the breeding season, the distinctive contribution of this study compared with previous gonadal-transcriptomic investigations in other Siluriformes lies not only in documenting sex-biased genes but also in providing a molecular foundation for developing non-lethal sex-identification methods for this morphologically indistinguishable species. A total of 303,192,896 raw reads were obtained, with an effective data rate of 98.4%, indicating high sequencing quality. Differential expression analysis identified 8694 genes, including 6369 upregulated in testes and 2325 upregulated in ovaries. Among these, 88 genes were functionally annotated as sex-related, with 62 testis-biased genes such as spata17, sox9, and dmrt1, and 26 ovary-biased genes including cyp19a, wnt8, and sox12. KEGG pathway enrichment analysis revealed that the TGF-β signaling pathway, insulin secretion, and steroid hormone biosynthesis may play crucial roles in gonadal development and differentiation in H. guttatus. The expression patterns of key genes such as hsd11b1, amh, and insl3 were validated by quantitative real-time PCR, showing consistency with the transcriptome results. These findings lay a molecular foundation for understanding the regulatory mechanisms of sex differentiation in H. guttatus, and provide candidate genes for further investigation into the genetic basis of gonadal development, which is essential for improving artificial reproduction and selective breeding practices. Full article

(This article belongs to the Special Issue Germplasm Resources and Genetic Breeding of Aquatic Animals)

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17 pages, 3912 KB

Open AccessArticle

Comparative Proteomic Profiling of a Virulent Wild-Type Nocardia seriolae and Its Attenuated Vaccine Strain

by Yao Yao, Weimei He, Li Wu, Lei Huang, Chengying Li, Yingying Tao, Xiaoyi Pan, Jianhong Shu, Yulong He, Jiayun Yao and Huapeng Feng

Fishes 2026, 11(1), 42; https://doi.org/10.3390/fishes11010042 - 9 Jan 2026

Viewed by 279

Abstract

Nocardia seriolae (N. seriolae) is a significant bacterial pathogen in global aquaculture, causing substantial economic losses. Live-attenuated vaccines represent a promising control strategy, but their molecular mechanisms remain poorly understood. This study employed a quantitative proteomic approach to compare the proteomic [...] Read more.

Nocardia seriolae (N. seriolae) is a significant bacterial pathogen in global aquaculture, causing substantial economic losses. Live-attenuated vaccines represent a promising control strategy, but their molecular mechanisms remain poorly understood. This study employed a quantitative proteomic approach to compare the proteomic profiles of a virulent wild-type strain (F1) and an attenuated vaccine strain (F110) of N. seriolae. Using a data-independent acquisition (DIA)-based LC-MS/MS analysis, we identified 4516 proteins, with 540 showing significant differential expression (311 upregulated, 229 downregulated). Bioinformatic analysis revealed that upregulated proteins in F110 were primarily involved in metabolic processes, including phosphatidate cytidylyltransferase and various enzymes related to amino acid and nucleotide metabolism. Conversely, downregulated proteins were enriched in virulence-associated functions, including HtpX and MFS transporter permease. These findings suggest that attenuation involves a complex reprogramming of metabolic pathways coupled with a reduction in key virulence factors, providing insights into the potential molecular basis of vaccine development and potential targets for novel therapeutic strategies. Full article

(This article belongs to the Special Issue Infection and Detection of Bacterial Pathogens in Aquaculture)

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32 pages, 4378 KB

Open AccessReview

Precision, Reproducibility, and Validation in Zebrafish Genome Editing: A Critical Review of CRISPR, Base, and Prime Editing Technologies

by Meher un Nissa, Yidong Feng, Shahid Ali and Baolong Bao

Fishes 2026, 11(1), 41; https://doi.org/10.3390/fishes11010041 - 9 Jan 2026

Viewed by 457

Abstract

The rapid evolution of CRISPR/Cas technology has transformed genome editing across biological systems in which zebrafish have emerged as a powerful vertebrate model for functional genomics and disease research. Due to its transparency, genetic similarity to humans, and suitability for large-scale screening, zebrafish [...] Read more.

The rapid evolution of CRISPR/Cas technology has transformed genome editing across biological systems in which zebrafish have emerged as a powerful vertebrate model for functional genomics and disease research. Due to its transparency, genetic similarity to humans, and suitability for large-scale screening, zebrafish is an appropriate system for translating molecular discoveries into biomedical and environmental applications. Thereby, this review highlights the recent progress in zebrafish gene editing, targeting innovations in ribonucleoprotein delivery, PAM-flexible Cas variants, and precision editors. These approaches have greatly improved editing accuracy, reduced mosaicism, and enabled efficient F0 phenotyping. In the near future, automated microinjections, optimized guide RNA design, and multi-omics validation pipelines are expected to enhance reproducibility and scalability. Although recent innovations such as ribonucleoprotein delivery, PAM-flexible Cas variants, and precision editors have expanded the zebrafish genome-editing toolkit, their benefits are often incremental and context-dependent. Mosaicism, allele complexity, and variable germline transmission remain common, particularly in F0 embryos. Precision editors enable defined nucleotide changes but typically exhibit modest efficiencies and locus-specific constraints in zebrafish. Consequently, rigorous validation, standardized workflows, and careful interpretation of F0 phenotypes remain essential. This review critically examines both the capabilities and limitations of current zebrafish gene-editing technologies, emphasizing experimental trade-offs, reproducibility challenges, and realistic use cases. Full article

(This article belongs to the Section Genetics and Biotechnology)

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Fishes, Volume 11, Issue 1 (January 2026) – 70 articles

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