Fishes doi: 10.3390/fishes11050291

Authors: Stephanie K. Venables Lukas Müller Christoph A. Rohner Andrea D. Marshall Jimmy van Rijn Nilza de Catarina John D. Filmalter Ryan Daly

Bull sharks (Carcharhinus leucas) are highly mobile coastal predators, whose broad movements complicate conservation planning, particularly in the Western Indian Ocean, where key habitats remain poorly understood. Using passive acoustic telemetry, this study assessed the habitat use, residency, and regional connectivity of adult bull sharks within the Bazaruto Seascape, Mozambique, evaluating the area’s ecological role within a wider movement network. Sharks tagged around Bazaruto exhibited high residency (mean Rmax = 0.45) and year-round presence, with core habitat concentrated along seaward reef systems and inshore areas off the San Sebastian Peninsula. Although most core habitat areas (82%) overlapped with existing marine protected areas, important habitats extended beyond protected area boundaries. In addition to supporting resident individuals, the seascape functioned as a seasonal waypoint within a regional movement corridor, with transient sharks exhibiting short periods (<5 days) of seasonal residency (primarily between May and November). Movement patterns revealed strong connectivity with other aggregation sites along the southeast African coast and occasional long-distance movements across the Mozambique Channel to Madagascar and beyond. These findings demonstrate that the Bazaruto Seascape provides both critical habitat and acts as a connectivity node for resident and transient bull sharks, highlighting the need for conservation strategies that combine local spatial protection with broader regional and transboundary management frameworks.

Fishes doi: 10.3390/fishes11050290

Authors: Kelsey C. James Jonathan M. Walker Brittany D. Schwartzkopf Emmanis Dorval Brad E. Erisman

Pacific sardine (Sardinops sagax) are an economically important forage fish in the Northeast Pacific Ocean that undergo large changes in abundance over decadal scales and exhibit high individual variation in somatic growth. Past studies have suggested that somatic growth in Pacific sardine may be density-dependent and vary regionally in response to environmental conditions. We analyzed somatic growth in Pacific sardine off the U.S. Pacific Coast during the recent period of low abundance (2012–2021) and compared the results to those of previous studies to evaluate evidence of spatial or temporal variation in growth. Sampled fish (n = 3228) ranged in length from 30 to 291 mm SL and in age from 0 to 9 years and displayed high individual variation in length-at-age and age-at-length. Length-at-age data were best explained by the von Bertalanffy growth model, and sample distribution simulations showed the dataset to be robust and unbiased. Estimated growth parameters (L∞ = 243, K = 0.795, t0 = −0.638) were consistent with an opportunistic life history strategy characterized by rapid growth, early maturation, and a short lifespan. While the estimated growth rate (K) was higher than in a previous study conducted during a period of high abundance and indicated that growth may be density-dependent, the parameter estimates from the previous study were influenced by sample distribution bias. Similarly, differences in study region, season, collection method, aging methods, and other factors precluded any definitive conclusions on the source of reported differences in growth patterns among studies.

Fishes doi: 10.3390/fishes11050289

Authors: Raquel S. F. Vieira Cláudia A. Rocha Carlos A. S. Venâncio Luís M. Félix

During production, fish are exposed to multiple environmental, physiological, and physical stressors, which compromise development, productivity, and welfare and urge the implementation of effective and safe stress-mitigating strategies, particularly during early developmental stages. Larval zebrafish (Danio rerio) constitute a powerful model for studying acute stress responses due to the numerous advantages they offer, such as developmental transparency, a conserved hypothalamic–pituitary–interrenal (HPI) axis, and suitability for high-throughput screening. This review examines the potential of natural monoterpenes as stress-reducing compounds and compares their performance with conventional synthetic anesthetics. Evidence from vortex-flow stress paradigms, behavioral profiling and biochemical assays shows that acute stress in zebrafish larvae triggers metabolic disruption, behavioral hyperactivity and enzyme imbalance, with cortisol responses depending on stimulus intensity. Monoterpenes such as thymol and menthol consistently reduce stress-induced hyperactivity, support redox homeostasis and display favorable safety profiles at low doses and short exposures. Nevertheless, as research into these substances is still recent, evidence of any potential adverse effects is still limited. Although individual monoterpenes may act on different subsets of molecular targets, their multimodal mechanisms, including gamma-aminobutyric acid (GABA)ergic enhancement, voltage-gated ion channel and transient receptor potential (TRP) modulation, suggest broader and potentially safer actions compared to single-target anesthetics as tricaine methane sulfonate (MS-222). Collectively, these findings suggest that monoterpenes offer promising natural alternatives for stress mitigation in aquaculture and the refinement of research procedures involving early life stages.

Fishes doi: 10.3390/fishes11050288

Authors: César Santificetur Rodolfo Miguel Silva Ana Méndez Jorge Pisonero Alberto Teodorico Correia

Understanding the life-history strategies of deep-sea fishes is essential for improving ecological knowledge and informing conservation efforts. Using otolith microchemistry, this study reconstructed the ontogenetic movement patterns of four grenadier species (Nezumia aequalis, Hymenocephalus billsam, Coelorinchus marinii, and Malacocephalus occidentalis) caught in the continental slope off southern Brazil (Southwestern Atlantic). Elemental signatures (Ba:Ca, Sr:Ca, Li:Ca, Mg:Ca, Mn:Ca, Ni:Ca, Cu:Ca, and Zn:Ca) were quantified along core-to-edge transects of sagittal otoliths using Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS). Ontogenetic shifts were identified using change-point detection (PELT). A general decline in elemental incorporation with age was observed across species, consistent with ontogenetic physiological regulation. Species-specific multi-elemental patterns suggest distinct ecological strategies. Nezumia aequalis exhibited an abrupt decline in Ba:Ca, indicating an early-life environmental shift. Hymenocephalus billsam showed increasing Ba:Ca and Sr:Ca profiles, consistent with continued use of pelagic-associated water masses. Coelorinchus marinii and Malacocephalus occidentalis displayed more complex patterns, with the latter showing pronounced Ba:Ca and Zn:Ca peaks that may reflect mid-life habitat shifts or physiological events. Mn:Ca ratios differed between pelagic and demersal species. Otolith microchemistry combined with change-point analysis could provide insights into deep-sea fish ontogeny, although interpretations should consider both environmental and physiological influences.

Fishes doi: 10.3390/fishes11050287

Authors: Tetsuro Sugai Katsuji Morioka Kohsuke Adachi

Collagen (ASC) was purified from four flatfish species (Greenland halibut, blackfin flounder, stone flounder, and slime flounder) collected from a cold area in Japan to investigate their biochemical properties. Sodium dodecyl sulfate–polyacrylamide gel electrophoresis pattern, Fourier transform infrared spectroscopy, and circular dichroism analysis revealed the typical structure of type I collagen. The denaturation temperature (Td) of ASC positively correlated with the physiological temperature (Tp) using previously reported data, which were obtained from fish (a total of 32 species). In this study, the lowest hydroxyproline (Hyp)/Pro/imino acid (Pro + Hyp) content was observed in Greenland halibut ASC (Tp is lowest), whereas the highest Ser content was observed in slime flounder ASC (Tp is highest). Using the data obtained from a previous study, a positive/negative correlation could be found between Td and Hyp/Ser, which is consistent with our previous reports. The Pro content in the present data followed the pattern of Hyp but exceeded the value predicted from Td by approximately 30 residues. These results may suggest that the collagen extracted from four flatfish in the cold area adopted decreasing imino acid content and increasing serine content for their adaptation.

Fishes doi: 10.3390/fishes11050286

Authors: María de Lourdes Jiménez-Badillo

More than 30,000 species of bony fishes, sharks and rays have been identified worldwide [...]

Fishes doi: 10.3390/fishes11050285

Authors: Chaojie Zhu Ziling Song Zhengwei Ye Yanjiao Zhang Jiahao Liu Lindong Xiao Chenchen Bian Qiang Ma Yuliang Wei Mengqing Liang Houguo Xu

Our previous studies found that lipid emulsifiers can promote the absorption and deposition of liposoluble pigments in shrimp. The present study aimed to further investigate the effects of liposoluble pigments lutein (LUT) and lycopene (LYC), and their combination with lysophospholipids (LPL), on the growth performance, body coloration, and lipid composition of Pacific white shrimp Penaeusvannamei. Five diets were formulated: a control diet (Control), Control + 0.02% lutein (LUT), Control + 0.02% lycopene (LYC), LUT + 0.1% LPL (LUT + LPL), and LYC + 0.1% LPL (LYC + LPL). The feeding trial lasted for 8 weeks. There were no significant differences in shrimp growth and body composition among all groups. Both LUT and LYC increased the redness (a*) and yellowness (b*) of cooked shrimp. LPL synergistically enhanced the pigmentation-improving effects of LUT but weakened those of LYC. Additionally, LYC decreased the redness and yellowness of raw shrimp. Both LUT and LYC reduced the contents of saturated fatty acids and EPA while increasing the DHA content; LPL further enhanced this modulatory effect. In conclusion, LPL acts synergistically with LUT to improve the body coloration and modify the fatty acid composition of Pacific white shrimp, but its effect with LYC is limited.

Fishes doi: 10.3390/fishes11050284

Authors: Daniel Montero Samira Sarih Marta Carvalho Félix Acosta Luís Monzón-Atienza Alvaro Gordillo Ehab Aboelsaadat Silvia Torrecillas

As aquaculture adopts more sustainable feed formulations, interest in functional feed additives has grown to help mitigate the health and performance challenges associated with low-marine-ingredient diets. This study evaluated the effects of dietary supplementation with a commercial blend of mono-, di-, and triglycerides of short- and medium-chain fatty acids (SCFAs and MCFAs; BalanGUT™ AQ P, BASF) on growth, health, and disease resistance to Vibrio anguillarum in juvenile gilthead sea bream (Sparus aurata) fed practical low fishmeal and fish oil diets. Over an 8-week trial, fish were fed diets containing 0.3%, 0.5%, or 1% of a glyceride blend of SCFAs and MCFAs (BalanGUT™ AQ P) or a Control diet without functional additive supplementation. Growth performance and feed utilization were not affected by the supplementation of SCFAs/MCFAs glycerides, although non-significant trends (p > 0.05) toward improved specific growth rate (up to 12%) and reduced feed conversion ratio (up to 17%) were observed in sea bream fed supplemented diets, particularly during the 4 initial weeks and at the highest inclusion level (1%). Moderate (0.5%) and high (1%) supplementation levels of SCFAs and MCFAs significantly improved survival following Vibrio anguillarum challenge, despite no significant changes being observed in general systemic innate immune markers, such as serum lysozyme or ACH50 activities. SCFAs/MCFAs supplementation, particularly at 0.3% or 0.5%, also modulated intestinal morphology, including thinner submucosa and smaller goblet cell area in the posterior intestine, suggestive of a more homeostatic mucosa and reduced basal inflammation when feeding a low-FM/FO-based diet. These results suggest that the protective effects of this SCFAs/MCFAs glyceride blend are mediated primarily through local rather than systemic immune modulation. Overall, this study supports the use of functional SCFAs and MCFAs glyceride blends as a functional strategy to promote resilience and health in fish fed sustainable, low-marine-ingredient diets.

Fishes doi: 10.3390/fishes11050283

Authors: Can Cui Dezhen Li Fuzhi Zu Dejun Feng Xiaoyu Qu Yi Tao

Proper configuration of aeration tubes is crucial for improving water quality and promoting the welfare and growth of cultured organisms in Recirculating Aquaculture Systems (RASs). To investigate the effects of aeration tube shapes (arc-shaped, disc-shaped, and linear-shaped) and positions (d = r, 1/2r) on performance, this study conducted experiments in a circular RAS tank. Methodologically, feed pellets were used to simulate solid waste, while ink was added to visualize the flow field, and mixing performance was quantitatively assessed using the spatial distribution uniformity. The results indicated that without aeration, the physical presence of the tubes affected waste collection but had minimal impact on water mixing. Under aeration conditions, placing tubes at d = 1/2r instead of d = r resulted in more efficient waste collection and improved water mixing. Waste collection performance was ranked as arc-shaped > disc-shaped > linear-shaped, whereas water mixing performance ranked linear-shaped > arc-shaped > disc-shaped. It is therefore recommended to place arc-shaped aeration tubes at d = 1/2r to achieve optimal overall performance. These findings provide valuable baseline insights into the selection and placement of aeration devices, offering preliminary practical guidance for aquaculture engineering.

Fishes doi: 10.3390/fishes11050282

Authors: Maria J. Bebianno Mustafa Tuncsoy Thiago L. Rocha Tania Gomes Taina Garcia

The increasing production of diverse applications of engineered nanoparticles along with their potential release into the marine environment from both point and diffuse sources have become a significant concern for ocean health. Due to their unique physical properties, particularly their high surface-to-volume ratio, these nanoparticles can exhibit enhanced bioavailability and toxicity to marine biota. Copper oxide nanoparticles (CuO NPs) are especially prevalent due to their wide range of commercial applications. In the aquatic environment, these nanoparticles typically become part of colloidal fraction and are subjected to physicochemical transformations, leading to the formation of aggregates that eventually sink and deposit onto the bottom substrate. Therefore, sediments, in addition to the water column, act as the primary route of exposure to benthic organisms. The clam Rudipates decussatus is a marine suspension-feeder of great ecological and economic importance in Europe. Ruditapes decussatus were exposed to CuO NPs (10 μg L−1) or an equivalent concentration of ionic copper (Cu2+) in both water and water/sediments matrices for 15 days to compare the toxicological impact of different exposure routes. Copper accumulation was monitored in both gills and digestive gland, alongside various biomarkers of susceptibility, exposure, and damage. The results revealed distinct uptake patterns that were dependent on the exposure routes, the chemical form of the metal and the specific tissue responses. Highlighting the complex impact of these contaminants on marine biodiversity.

Fishes doi: 10.3390/fishes11050281

Authors: Jose Carlos Campos-Sánchez Francisco A. Guardiola María Ángeles Esteban

Arnica (Chiliadenus glutinosus (L.) Fourr.) is an endemic plant widely used in Spanish traditional medicine as infusions and alcoholic macerates for different ailments. Despite this use, information about the biological activity of these preparations in fish-related models is scarce. In the present study, the arnica extract bioactivity assay evaluated aqueous, ethanolic, and methanolic extracts at different doses (0, 0.001, 0.01, 0.125, 0.25, 0.5, and 1 mg mL−1) to compare their antioxidant activity, effects on four marine fish pathogens (Vibrio harveyi, Vibrio anguillarum, Photobacterium damselae and Tenacibaculum maritimum), cytotoxicity on the PLHC1 tumour cell line, and their impact on immunological parameters in head-kidney leucocytes (HKLs) of gilthead seabream (Sparus aurata). All extracts showed dose-dependent antioxidant activity, while bactericidal effects depended on the solvent and were mainly observed at the highest concentrations. Ethanolic and methanolic extracts displayed clear cytotoxicity, whereas the aqueous extract showed lower toxicity and was selected for further evaluation. In the carrageenan stimulation assay, selected concentrations (0, 0.25, and 0.5 mg mL−1) of the aqueous extract were tested in leucocytes stimulated with λ-carrageenan (0 and 1000 µg mL−1), and respiratory burst and phagocytic activity, cell morphology, and gene expression were analysed. The aqueous extract reduced respiratory burst and phagocytic capacity in activated leucocytes and was associated with morphological signs of cell activation. It also downregulated crel and casp9 expression. These results provide a comparative view of the in vitro bioactivity of different traditional preparations of arnica and show that their biological effects strongly depend on the solvent used and the concentration tested, providing initial experimental information on their cellular effects in fish.

Fishes doi: 10.3390/fishes11050279

Authors: Danielle Alves da da Silva Flávia Abreu Everton Gisely Karla de Almeida Costa Suzianny Maria Bezerra Cabral da da Silva Fernando Leandro dos dos Santos Rodrigo Antônio Ponce de Leon Ferreira de Carvalho Giovanni Sampaio Gonçalves João Fernando Albers Koch Luis Otavio Brito

The present study investigated how dietary inclusion of solubilized mannan oligosaccharide (MOS) influences growth performance, digestive health, stress resilience, and production profitability in Pacific white shrimp (Penaeus vannamei) reared under intensive synbiotic conditions. Juveniles averaging 3.00 ± 0.04 g were stocked at 100 shrimp m−2 and fed experimental diets containing 0 (control), 1.0, 2.0, or 4.0 g kg−1 MOS for 60 days. Shrimp receiving 1.0 g kg−1 MOS showed higher growth rate, improved feed conversion, and greater final body weight than the control (p < 0.05), indicating enhanced feed utilization efficiency and better overall performance. Gut morphology improved in MOS-fed treatments, with increased mucosal fold height and enterocyte height, suggesting increased nutrient absorption and improved gut functionality. Gut presumptive total count remained relatively stable among treatments, although Bacillus counts tended to increase with solubilized MOS supplementation. Under ammonia and nitrite stress, supplemented groups showed higher survival and reduced gill damage, indicating improved physiological tolerance and health status. Economic analysis demonstrated that 1.0 and 2.0 g kg−1 MOS achieved the best cost–benefit ratios under intensive conditions. Overall, moderate MOS supplementation enhanced growth, gut morphology, stress resistance, and economic efficiency. Polynomial regression analysis, based on the four dietary inclusion levels evaluated, suggested that approximately 1.5 g kg−1 MOS may represent an estimated optimal inclusion level.

Fishes doi: 10.3390/fishes11050280

Authors: Jiawen Li Weidong Zhang Shengzhao Xiao Xuanzhong Chen Yuesheng Huang Jujian Lv Kaihan Lin Xianglei Hu Xianxian Zeng Rongjun Chen

Efficient detection of fish diseases is essential for intelligent health monitoring and timely intervention in aquaculture. However, current computer vision models remain computationally intensive, hindering their deployment on resource-constrained edge devices in aquaculture applications. To this end, this study developed a lightweight detection framework based on an improved You Only Look Once (YOLO), aiming to achieve a favorable balance between detection accuracy and on-site inference efficiency. First, a Dual-Branch Feature-Preserving Downsampling (DFPD) module was proposed to enhance the extraction of valuable disease-related cues with minimal computational overhead. Subsequently, structured pruning was applied to compress the optimized baseline model. Four pruning techniques, including Slim, GroupTaylor, Layer-Adaptive Magnitude-Based Pruning (LAMP), and L1-based, were evaluated under the same conditions. The enhanced baseline model improved precision from 0.864 to 0.908 and mAP@0.5:0.95 from 0.613 to 0.632, while already reducing the Number of Parameters (Params) and Giga Floating-point Operations Per Second (GFLOPs) compared with the original YOLOv8n. Among the pruning techniques, L1-based produced the best overall trade-off, yielding a final model that maintained a F1-score of 0.860 while reducing Params and GFLOPs by 54.7% and 49.4%, respectively, relative to the original detector. Ablation studies further revealed that a moderate FLOPs reduction of approximately 41% to 47% was optimal for preserving diagnostic performance while enhancing compactness. Edge deployment tests on an RK3588S device verified the framework’s practical inference speed advantage. Therefore, this study offers a deployment-friendly computer vision solution for on-site fish disease detection in aquaculture management, particularly suited to real-world scenarios with limited computational resources.

Fishes doi: 10.3390/fishes11050278

Authors: İhsan Çelik Pınar Çelik Tolga Göksan

In this study, the effects of different feeds provided during the initial feeding period of Trichogaster lalius (dwarf gourami) larvae on larval survival were evaluated. Larvae reared under laboratory conditions were assigned to four dietary treatments (EY: boiled chicken egg yolk, RO: live rotifers, IN: infusoria, SP: live Spirulina) during days 3–5 post hatching, after which all groups were enriched with live Artemia on days 5–10. A total of 4800 larvae were distributed across 16 treatment groups. On day 10, larval abundance and total length (mm) were recorded, and survival percentages were subsequently calculated. The pooled survival rates at the end of the experiment were 95.50 ± 4.05 for EY, 95.50 ± 2.53 for RO, 58.58 ± 8.88 for IN, and 77.25 ± 10.23 for SP. Statistical analysis revealed no significant differences in survival between the EY and RO groups (p > 0.05). In contrast, significant differences were observed between the IN group and the SP group, as well as between IN and the remaining treatment groups (p < 0.05). Moreover, no significant differences in total length were detected among the 16 groups at the end of the experiment (p > 0.303). Overall, the findings suggest that, under the present experimental conditions, larval survival of T. lalius was higher in the egg yolk and rotifer feeding treatments than in the infusoria and live Spirulina groups.

Fishes doi: 10.3390/fishes11050277

Authors: Archontia Chatzispyrou Konstantinos Charalampous Evgenia Lefkaditou Aikaterini Anastasopoulou Constantin Koutsikopoulos

The feeding ecology of sympatric elasmobranchs provides key insights into trophic interactions and species coexistence within demersal ecosystems. The current study examined the diet composition and trophic relationships of three skate species (Raja asterias, Raja clavata, and Raja miraletus) in the eastern Ionian Sea (central Mediterranean). Stomach content analysis was combined with quantitative dietary indices and multivariate statistical approaches, including NMDS, PERMANOVA, SIMPER, and Schoener’s overlap index. All skate species primarily consumed benthic crustaceans and demersal teleost fishes, although differences in prey contribution were detected among species. Raja clavata exhibited higher prey diversity, whereas R. asterias and R. miraletus showed stronger reliance on decapod crustaceans. Multivariate analyses revealed significant interspecific differences in diet composition with generally low-to-moderate trophic overlap among species. These findings suggest that sympatric Rajidae species exploit similar prey resources while maintaining partial trophic partitioning, possibly reducing direct niche overlap and facilitating ecological coexistence. This study contributes to the understanding of trophic structuring in Mediterranean skate assemblages and supports ecosystem-based approaches to demersal fisheries management.

Fishes doi: 10.3390/fishes11050276

Authors: Sisi Huang Famou Zhang Heng Zhang Ming Gao Kangbo Li

Chub mackerel (Scomber japonicus) is a key pelagic commercial fish species in the North Pacific Ocean and is one of the priority species managed by the North Pacific Fisheries Commission (NPFC). This study assessed the stock status and maximum sustainable yield (MSY) of S. japonicus using the Length-based Bayesian Biomass (LBB) estimator and the Catch-MSY model. The assessment was based on length-frequency data collected from the light purse seine fishery on the high seas of the North Pacific (6061 individuals sampled during April–December, 2019–2024) combined with historical catch data spanning 1995 to 2024. Management implications were further analyzed using the Kobe plot and the Kobe II Strategy Matrix (K2SM). The results showed that: (1) The LBB model revealed significant interannual variability in stock status of S. japonicus. Although the stock was within sustainable limits (B/BMSY ≥ 1.0) in 2019, 2021, and 2022, it suffered from overfishing or was heavily overfished in 2020, 2023, and 2024. Notably, integrated data analysis indicated that during 2023–2024, the B/BMSY ratio dropped to 0.51, reflecting a marked deterioration in the stock condition. (2) The Catch-MSY model estimated the maximum sustainable yield (MSY) at 278,000 t, with a 95% confidence interval (CI) ranging from 162,000 t to 475,000 t. (3) Based on catch data, the Kobe plot indicated that in the final assessment year, the probability of the stock being in a sustainable state was only 23.2% at the 95% confidence level. The probabilities of being recruitment-overfished, fishing-overfished, and severely overfished were 37.6%, 14.9%, and 24.3%, respectively. With relative biomass B/BMSY < 1 and relative fishing mortality F/FMSY < 1, the stock status in the final assessment year was diagnosed as recruitment overfishing. (4) Integrating the outputs of the two models, the Kobe plot, and the probabilistic projections of future stock status from the Kobe II Strategy Matrix (K2SM), it is recommended that the total allowable catch (TAC) be set within 60–80% of the baseline TAC during the medium-term management phase (5–10 years), corresponding to a range of 211,300 t to 281,700 t. In the long term, if the stock exhibits positive recovery trends, the TAC could be gradually increased to the MSY level to achieve the maximum sustainable utilization of this fishery resource.

Fishes doi: 10.3390/fishes11050275

Authors: Yi Tian Junwei Chen Yudi Zhao Jiawei Zhong Haotian Xue Xin Wei Qiang Gao

Low-salinity stress poses a critical constraint on commercial aquaculture and the survival of the sea cucumber (Apostichopus japonicus). This study investigated the regulatory network involving lncRNA011760, miR-novel-91, and their target gene NIPA2 in response to salinity fluctuations. Using integrated in vivo and in vitro functional assays, we demonstrate that lncRNA011760 acts as a competitive endogenous RNA (ceRNA) to sponge miR-novel-91, thereby alleviating the post-transcriptional repression of NIPA2. Based on these molecular dynamics, we propose a novel inhibition-adaptation-survival three-stage model. Initially (0–3 h), acute NIPA2 upregulation enhances Mg2+ transport efficiency to mitigate osmotic shock. During the mid-stage (3–24 h), miR-novel-91-mediated NIPA2 suppression creates a transient biosynthetic window, facilitating a shift from passive tolerance to active metabolic adaptation. Ultimately (24–48 h), lncRNA-driven NIPA2 restoration sustains Mg2+ homeostasis, allowing the organism to enter a low-metabolism survival mode. These stage-specific shifts reflect the inherent physiological strategies of sea cucumbers as osmoconformers.

Fishes doi: 10.3390/fishes11050274

Authors: Leilei Zhang Wei Fan Fenghua Tang Yongchuang Shi Shengmao Zhang

Accurate prediction of fishing grounds plays a crucial role in supporting the efficient operation of ocean-going fishing vessels. Based on catch data of Chub Mackerel (Scomber japonicus) and multiple concomitant oceanographic variables from 2014 to 2022 in the Northwest Pacific Ocean, we employed four machine learning methods, including Random Forest (RF; scikit-learn v1.7.2), Extreme Gradient Boosting (XGBoost; xgboost v3.1.3), Light Gradient Boosting Machine (LightGBM; lightgbm v4.6.0) and Categorical Boosting (CatBoost; catboost v1.2.8), to construct a prediction model for high-abundance fishing grounds of Chub Mackerel. After selecting the optimal model through evaluation metrics, we applied the SHapley Additive exPlanations (SHAP; shap v0.44.1) method to visualize and interpret the optimal model, quantifying the importance of environmental factors on high-abundance fishing grounds, thus enhancing the interpretability and credibility of the machine learning model. The results indicated that the catch exhibited significant fluctuations at both interannual and intramonthly scales (p < 0.05). The annual catch showed a phased increasing trend, peaking in 2017 and 2018. Monthly catches were highest in September and October. Evaluated against established performance metrics, the RF model demonstrated the highest predictive performance with the highest values of accuracy and F1-score, 76.33% and 77.73%, Precision 72.81%, Recall 83.36%, ROC-AUC 0.8393, respectively, and was therefore selected as the most suitable for predicting Chub Mackerel fishing grounds. SHAP analysis identified the temporal variables year and month as the most influential predictors, followed by chlorophyll-a concentration (Chl-a), sea surface salinity (SSS), and sea surface temperature (SST). SHAP analysis can comprehensively reveal the degree and direction of influence of each variable at both global and local levels. These findings indicate that integrating machine learning with explainability techniques can enhance the scientific robustness and transparency of fishing ground forecasts, providing data-driven support for ecosystem-based fishery management.

Fishes doi: 10.3390/fishes11050273

Authors: Tianwei Wang Yongxiang Yu Chunyuan Wang Yingeng Wang Zhiqi Zhang Xiaojun Rong Meijie Liao Kun Hu Zheng Zhang

The inappropriate use of antibiotics in aquaculture has exacerbated antimicrobial resistance in pathogens, thereby reducing the efficiency of aquaculture production. Therefore, it is crucial to develop effective antibiotic alternatives capable of inhibiting pathogenic bacteria. Against this background, the present study investigated the efficacy and underlying mechanism of carvacrol against Vibrio harveyi in the mariculture of the marine fish Sebastes schlegelii, aiming to provide data support for the development of green fishery drugs to replace antibiotics. The results indicated that pre-treatment with carvacrol increased the survival rate of infected S. schlegelii. Meanwhile, post-infection administration of carvacrol alleviated intestinal pathological damage. Carvacrol regulated host immunity by modulating the transcription of the immune-related genes NF-κB/RelA and IL-15. Carvacrol did not significantly alter the activities of SOD, MDA, or CAT, suggesting that the oxidative defense pathway was not primarily involved. Analysis of intestinal Vibrio load confirmed that carvacrol could inhibit the growth and colonization of intestinal Vibrio, thereby maintaining microbial homeostasis. Immunohistochemistry and peripheral blood flow cytometry showed that carvacrol enhanced the adaptive immunity of fish by increasing the proportions of CD4-1+ T cells and CD79a/CD79b+ B cells in tissues and peripheral blood. In conclusion, carvacrol enhances the resistance of S. schlegelii against V. harveyi by inhibiting pathogenic bacteria, improving intestinal morphological structure, reducing pathogenic bacterial load to maintain microbial homeostasis, and enhancing the adaptive immunity of the organism. This study provides a theoretical basis and data support for the substitution of antibiotics and the development of green feed additives in aquaculture.

Fishes doi: 10.3390/fishes11050272

Authors: Niki Milatou Odysseas Papadopoulos-Michalas Persefoni Megalofonou

Marine anthropogenic particle pollution is a major environmental concern due to its persistence and widespread distribution. Microplastics are widely recognized as a subset of anthropogenic particles originating from synthetic polymers. This study examines the occurrence, characteristics, and biological associations of anthropogenic particles ingested by Atlantic chub mackerel from the Saronikos Gulf. A total of 179 specimens were analyzed for anthropogenic particles in the gastrointestinal tract, while muscle tissue was examined in 51 individuals. Anthropogenic particles were detected in the gastrointestinal tract of 74% of individuals and were also present in muscle tissue in 41% of the analyzed specimens. Fibers were the dominant particle type, representing approximately 60% of the identified particles, followed by fragments at 40%. The majority of particles were micro-sized (<5 mm), although meso- and macro-sized particles were also recorded. Black-colored particles predominated, accounting for approximately 53% of the total. No significant differences in anthropogenic particle abundance were observed between sexes, and no consistent seasonal patterns were detected, except for higher occurrence in early autumn compared to winter, although this result should be interpreted with caution due to uneven sample sizes among sampling periods. No statistically significant correlations were found between anthropogenic particle abundance in the gastrointestinal tract or muscle tissue and fish size, condition factor, or stomach fullness. Overall, the findings highlight this species as a suitable bioindicator for monitoring anthropogenic particle pollution and provide baseline information for future assessments in the Saronikos Gulf. Particle identification was based on visual characterization without spectroscopic confirmation; therefore, the detected particles are considered anthropogenic and their polymer composition could not be definitively confirmed.

Fishes doi: 10.3390/fishes11050271

Authors: Talha Laique Mikkel Gunnes Ole Folkedal Jonatan Nilsson Evelina A. L. Green Hannah Normann Gundersen Øyvind Øverli Habib Ullah

Intensive salmon farming is associated with high mortality rates, highlighting the need for new welfare indicators that can detect adverse conditions earlier and less invasively than many current approaches. Existing animal-based indicators used in the industry typically depend on subjective scoring and provide information mostly after welfare problems have already developed, thereby raising questions about their efficacy. Examples include emaciation, wounds, or scale loss, etc. Preliminary data and ongoing investigation suggest that melanin-based skin pigmentation may change dynamically with stress and condition in salmonid fishes. In this study, we present a semi-automated methodology for assessing changes in the grayscale intensity of melanin-based skin spots within the operculum region of adult Atlantic salmon (Salmo salar) kept in seawater. The pipeline combines computer vision models to detect the operculum, segment individual spots, and extract grayscale-based features for spot-level analysis over time. The method was applied to out-of-water images collected before and after exposure to a confinement episode. The results showed an overall shift in grayscale intensity from black to pigmentation fading after the challenge, although responses varied among individuals. These findings indicate that the proposed methodology can detect temporal changes in opercular melanin-based spots under applied experimental conditions. We therefore present this work as proof of principle for using computer vision to quantify changes in melanin-based skin spots as a potentially useful, non-invasive indicator of stress and welfare in Atlantic Salmon.

Fishes doi: 10.3390/fishes11050269

Authors: Qi Huang Yongjun Sun Linlin Zhao Wenbo Zhu Fei Shao Jin Xu Yongjian Qin

The green sea turtle (Chelonia mydas), a widely distributed species, plays a crucial role in maintaining the marine ecosystem. However, studies on C. mydas require accurate and comprehensive genome annotation information. Long-read direct transcriptome data of C. mydas were obtained using direct RNA sequencing on the Oxford Nanopore Technologies (ONT) platform from blood tissue of a single captive individual. A total of 4061 novel transcripts were obtained by comparing long-read direct transcripts with genome annotation of C. mydas. We also predicted 2402 CDSs on the novel transcripts. Among them, 1208 (50.29%) had functional annotation information in the databases. In addition, we predicted and analyzed AS events, fusion transcripts, methylation sites, poly(A)s, and lncRNAs in the C. mydas long-read direct transcriptome. Overall, our study provides the a long-read direct blood transcriptome for C. mydas to complement and improve its genome annotation. This valuable resource will contribute to future research on C. mydas. Additionally, the analyses of transcriptome structure mentioned above may provide new insights and ideas for the study of C. mydas.

Fishes doi: 10.3390/fishes11050270

Authors: Guangyao Li Chunlei Feng Yongchuang Shi Keji Jiang Shenglong Yang

To accurately predict the fishing intensity of the Northwest Pacific squid fishing grounds and address the limitations of traditional models in capturing long-term temporal and spatial correlations and neglecting the coupling relationships of deep environmental factors, this study constructs a 3DCNN model and three fusion models incorporating residual, attention, and Transformer mechanisms. Using the 2017–2024 AIS fishing data and ocean environmental variables from the North Pacific squid fishing industry, the models’ performance is compared at 12 different temporal and spatial scales, and key core environmental variables are identified. The results show that the ResNet3D model exhibits the best overall performance, achieving an F1 score of 0.7909 at the 1.0°-7 days temporal–spatial scale. The residual connections effectively mitigate the gradient vanishing problem, balancing prediction accuracy and stability. The optimal spatial resolution is 1.0°, and the key environmental variables include S100, Chl-a100, PP100, and DO100. S100 is the core driving variable, consistently exhibiting the highest feature importance value at all time scales. It should be noted that Chl-a is considered an indirect indicator of primary productivity, which may influence squid distribution through trophic transfer processes rather than direct biological effects. This study demonstrates the prediction accuracy and applicability of the multi-mechanism fusion 3DCNN model, reveals the temporal and spatial distribution patterns of fishing intensity in the Northwest Pacific squid fishing grounds, and provides scientific methods and technical support for dynamic monitoring, intelligent management, and sustainable utilization of squid resources.

Fishes doi: 10.3390/fishes11050268

Authors: Jorge Homero Rodríguez-Castro Sandra Edith Olmeda-de la Fuente Jorge Alejandro Rodríguez-Olmeda Ulises de Jesús Balderas-Mancilla Juventino Tovar-Ortíz Jose Antonio Rangel-Lucio Luis Antonio Vázquez-Ochoa

Artisanal fisheries in Mexico frequently operate with limited data, lacking historical catch and effort series. In this context, the population status of the dogfish (Rhizoprionodon terraenovae) was evaluated for the first time in Priority Marine Regions 45–46 and the area of influence of the Wetland of International Importance Playa Tortuguera Rancho Nuevo, Tamaulipas, using methods based on size frequencies. Between November 2018 and February 2020, 541 artisanal fishing organisms were analyzed in La Barra del Tordo using FISAT II. The von Bertalanffy growth parameters for combined sexes were: L∞ = 105 cm, k = 0.59 years−1, t0 = −0.195 years. Total (Z), natural (M) and fishing (F) mortalities were 4.13, 0.467 and 3.22 years−1, respectively. The average exploitation rate (E = F/Z) was 0.78 (95% CI: 0.745–0.805), exceeding the reference point of 0.5 (G) indicating severe overexploitation. The parameters showed biological consistency (Ø′ = 3.81; M/k = 0.79), and natural mortality was within the range reported for the species. This finding, in a priority region for conservation under the regime of the Conservation Sector of the Marine Ecological Management Program, shows the urgent need to implement fisheries management with an ecosystem approach that guarantees the sustainability of the fishery and the integrity of the coastal ecosystem. The study demonstrates that, even with limited data, it is possible to obtain robust estimates to inform management decisions in natural protected areas

Fishes doi: 10.3390/fishes11050267

Authors: Youhai Du Silei Xia Wuxiao Zhang Wenping Yang Yebing Yu Zhaoxia Li Bin Peng Yude Wang Bo Liu Hongyan Tian Jianhua Ming

The purpose of this study was to investigate the effects of different feeding-promoting substances added to high plant protein diets on the growth, antioxidant, serum biochemical parameters, immune, and feeding-related genes of Procambarus clarkii. A total of 450 crayfish (3.94 ± 0.03 g) were selected and randomly divided into six groups, with each group consisting of three replicates and 25 crayfish per replicate. The crayfish were fed a basal diet without attractant (control group) and five experimental diets supplemented with 0.4% betaine (BET), 0.4% trimetlylamine oxide (TMAO), 0.4% squid paste (SQU), 0.4% dimethyl-β-propiothetin (DMPT), and 0.4% taurine (TAU). The feeding trial lasted for 6 weeks. The results showed that compared with the control group, the BET, SQU, DMPT, and TAU groups significantly improved in growth performance, weight gain rate, and specific growth rate of crayfish. Compared with the control group, the BET, MTAO, and SQU groups significantly increased hepatopancreas SOD, CAT, and T-AOC. Histological results showed that compared with the control group, all feeding attractant groups could alleviate hepatopancreas tissue damage. Compared with the control group, the TMAO and SQU groups significantly reduced serum GLU content as well as ACP and AKP activities. The results of gene quantitative analysis showed that, compared with the control, TMAO significantly upregulated the expression of tlr, nf-kb, propo, hsp70, and tgf-β, while TAU significantly increased the expression of hsp70, hsp90 and nf-kb genes. Compared with the control group, the expression levels of tor, 4ebp1, and s6k1 in the TMAO group were significantly increased. Compared with the control group, the expression levels of leptin and npy genes in the DMPT group were significantly increased. In summary, the addition of attractants to high plant protein feed has the effects of promoting growth, enhancing antioxidant capacity, improving digestive enzyme activity, alleviating hepatopancreas injury, improving immunity, and promoting feeding.

Fishes doi: 10.3390/fishes11050266

Authors: Santiago P. Aubourg Marcos Trigo Lina Pena Denis M. Andriamahefa Noa E. Rasoanaivo David Vieites Fanomezana M. Ratsoavina

Proximate composition, lipid classes, and fatty acid profile were comparatively analyzed in different body parts of carp (Cyprinus carpio) cultivated in Madagascar. Higher (p < 0.05) protein values (163.3–200.1 g·kg−1 range) were detected in muscle tissue (epaxial, hypaxial, and tail) than in the liver tissue (118.4 g·kg−1). The average lipid content showed the following decreasing tissue sequence: liver > hypaxial > tail > epaxial. The highest levels (p < 0.05) of phospholipids and sterols were obtained in the epaxial muscle part (94.0 and 24.0 g·kg−1 of lipids, respectively). A high presence of free fatty acids (183.2 g·kg−1 of lipids) was detected in the liver. In all tissues, α-tocopherol provided higher values (p < 0.05) than γ- and δ-tocopherol compounds; among body parts, the liver showed the highest levels (p < 0.05) for all tocopherols. Fatty acid (FA) groups revealed a higher range value (g·100 g−1 of total FAs) for monounsaturated FAs (48.19–52.57) than for saturated FAs (SFAs; 28.50–29.41) and polyunsaturated FAs (PUFAs; 17.96–22.57). The following increasing sequence was observed for ω3-PUFA/ω6-PUFA ratios in body parts: liver < hypaxial < tail < epaxial. All parts of muscle tissue contained higher (p < 0.05) PUFA/SFA values (0.72–0.77) than liver (0.61). Comparison of body parts revealed an inhomogeneous distribution of bioactive compounds. The liver tissue was found a good source of valuable constituents.

Fishes doi: 10.3390/fishes11050265

Authors: Zhongdian Dong

Anthropogenic pollution is among the most pervasive and persistent pressures affecting aquatic ecosystems worldwide, and fish are central to this issue not only because they are directly exposed to contaminants throughout their life cycle, but also because they connect environmental quality, ecosystem functioning, fisheries’ sustainability, and food safety [...]

Fishes doi: 10.3390/fishes11050264

Authors: Lang Xie Yan Pu Huatang Deng Huiwu Tian Dengqiang Wang Xinbin Duan Ziwei Shen Yunfeng Li

Environmental DNA (eDNA) metabarcoding has emerged as a powerful tool for biodiversity monitoring, yet its accuracy is fundamentally constrained by the completeness and taxonomic reliability of reference sequence databases. For the Three Gorges Reservoir (TGR), no integrated multi-marker eDNA reference library exists, hampering standardized fish conservation monitoring under the Yangtze River Ten-Year Fishing Ban. Here, we constructed a comprehensive, multi-marker eDNA reference database for the fish fauna of the TGR, encompassing mitochondrial 12S rRNA, 16S rRNA, and cytochrome c oxidase subunit I (COI) gene sequences from 173 specimens (120 species) collected between 2021 and 2024. After integrating publicly available sequences, the final database comprised 161 species. Then, we quantitatively compared species annotation performance between this local database and public repositories. Results showed that while public databases achieved higher nominal species coverage (94.67%), they exhibited critical deficiencies in annotation accuracy, correctly annotating only 77.97% (12S rRNA), 75.00% (16S rRNA), and 38.14% (COI) of sequences from shared species under controlled conditions. In contrast, the local database exhibited 92.37%, 93.10% and 100% annotation accuracy for the respective markers. Optimal interspecific Kimura 2-parameter (K2P) thresholds for species delimitation were 0.00448 (12S rRNA), 0.00531 (16S rRNA), and 0.00734 (COI). In addition, 15, 0, and 4 species pairs exhibited zero interspecific distance for 12S rRNA, 16S rRNA, and COI, respectively. These limitations reinforce the need for cautious interpretation of eDNA metabarcoding results and the integration of multiple markers or complementary nuclear loci. This study provides preliminary evidence that regionally curated, multi-marker reference libraries could improve taxonomic assignment reliability in eDNA metabarcoding compared to uncurated public repositories, providing a foundational resource for biodiversity conservation.

Fishes doi: 10.3390/fishes11050263

Authors: Fabíola Helena dos Santos Fogaça Nara Regina Brandão Cônsolo Eduardo S. Pina dos Santos Brenda S. de Oliveira Luísa Souza Almeida Leonardo Rocha V. Ramos Luiz Alberto Colnago

The global seafood industry faces persistent challenges related to product quality, safety, and authenticity, driven by complex supply chains, increasing demand, and the perishable nature of aquatic products. Traditional analytical methods often fall short in providing rapid, comprehensive, and non-destructive insights into the intricate biochemical changes occurring in seafood. 1H Nuclear Magnetic Resonance (1H NMR) spectroscopy has emerged as a powerful and versatile tool for metabolomics, offering a holistic view of the low-molecular-mass compounds (metabolites) present in biological samples. The present study applied 1H NMR for chemical fingerprint identification in mullets (Mugil liza) from Brazil. Dorsal muscle samples were taken from the fish during summer, autumn, and winter. The procedure involved freeze-drying the muscle tissue, thereafter extracting polar metabolites using designated solvents (methanol, water, and chloroform), and analyzing them using a 600 MHz spectrometer. As a result, 23 metabolites related to degradation biomarkers, essential metabolites, energy expenditure, and muscle structure were identified. The statistical analysis demonstrated a distinct separation between the geographical origins (RJ vs. SC), mostly influenced by variations in the concentrations of lactate, histidine, threonine, phenylalanine, and ornithine. Factors like fish size and seasonal variations did not markedly affect the overall metabolic profile, underscoring the reliability of these chemicals as stable origin indicators. The Principal Component Analysis identified two distinct groups of metabolites, establishing a profile for each geographical origin. The developed protocol can be applied to the processes of geographical identification. Thus, the 1H NMR tool was efficient in determining metabolites that can be considered biomarkers in analyses for seafood traceability.

Fishes doi: 10.3390/fishes11050262

Authors: Yuxiang Zhu Yueyue Fu Kai Liao Yang Liu Yang Zhang Jilin Xu

Dietary arachidonic acid (ARA) is essential for aquatic animal growth and health, but studies in bivalves are still limited. Here, microcapsule diets with increasing ARA concentrations (ARA1-6 groups: 0.35, 3.01, 5.25, 6.88, 8.69, and 10.27 mg g−1 dry matter) were prepared by spray drying, and clam Sinonovacula constricta juveniles were fed these diets for 14 days. Results showed that dietary ARA concentrations did not significantly affect clams’ survival, weight gain, and shell length gain rates. The clams in the ARA6 group had significantly higher crude lipid content than those in the other microcapsule groups. The ARA concentrations in the clams increased with higher dietary ARA, while n-3 polyunsaturated fatty acids (PUFAs) and eicosapentaenoic acid (EPA) concentrations decreased. The mRNA levels of cyclooxygenase 2 and 5-lipoxygenase type 2 were significantly higher in the ARA5 and ARA6 groups compared to the ARA1 group. The mRNA levels of 5-lipoxygenase type 3, toll-like receptor 4, and nuclear factor-kappa b p50 (nfκb p50) were significantly higher in the ARA6 group compared to the ARA1 group. As dietary ARA concentrations increased, the mRNA levels of glutamate–cysteine ligase catalytic subunit and glutathione S-transferase, along with malondialdehyde (MDA) content, increased in the clams. Additionally, the superoxide dismutase and catalase activities in the ARA5 and ARA6 groups were significantly higher than those in the ARA1 and ARA2 groups. Clam ARA content, acting as a central node, showed very strong positive correlations with MDA and cyclooxygenase 2, and very strong negative correlations with EPA and the n-3/n-6 PUFA ratio. Our results revealed that high dietary ARA, while not affecting growth, reduced the n-3/n-6 PUFA ratio and induced a response characterized by the upregulation of NF-κB and Nrf2 pathway genes in S. constricta.

Fishes doi: 10.3390/fishes11050261

Authors: Santa Purviņa Olga Revina Žanna Bertaite Kristofers Millers Rainers Džeriņš Justīne Padrevica Ruta Medne

This study evaluated the effects of a commercially produced, ready-to-use probiotic supplement, dominated by lactic acid bacteria, on the growth performance and selected health indicators of salmon (Salmo salar L.) fry, parr, and presmolts reared for restocking purposes. The results indicated a stage-specific response to probiotic application. In salmon fry, short-term immersion baths were associated with reduced juvenile mortality and improved tolerance to fluctuations in temperature and dissolved oxygen. In parr, immersion treatments were linked to improved growth performance, condition factor, and a lower incidence of gill-cover necrosis compared to the Control group. In presmolts, short-term dietary supplementation with probiotics was associated with increased growth rates relative to Controls. Probiotic application was associated with changes in bacterial isolates and, in some groups, lower antimicrobial resistance (AMR) indices, particularly after 14 days of immersion treatment. Probiotic supplementation was associated with improved growth and increased tolerance to environmental stressors, indicating its potential to support fish welfare and sustainable aquaculture.

Fishes doi: 10.3390/fishes11050260

Authors: Bo Zhan Zhiqiang Han

Based on previous studies and the ecological characteristics of Portunus trituberculatus, we hypothesized that climate change could substantially reshape its suitable habitat in Zhoushan fishing ground. Under present-day climate conditions (2010–2020), P. trituberculatus exhibits a distinct seasonal distribution pattern in this region. However, its potential spatial response to future climate change, and whether suitable habitat will remain available, remains poorly understood. To address this gap, we combined species occurrence records with environmental variables from the Bio-ORACLE v3.0 database, including benthic temperature, benthic salinity, benthic current velocity, primary productivity, bathymetry, topographic slope, and topographic aspect, to develop a maximum entropy (MaxEnt) model and predict the potential distribution of suitable habitat for P. trituberculatus under present-day conditions and future SSP1-2.6 and SSP2-4.5 scenarios for 2030–2040, 2040–2050, and 2090–2100. Model performance was high across all seasons, with area under the curve values exceeding 0.80. Primary productivity and benthic temperature were the dominant environmental predictors, highlighting the joint influence of trophic conditions and thermal constraints on habitat suitability. Future projections revealed pronounced seasonal reorganization of suitable habitat rather than a uniform range shift. Spring suitable habitat expanded consistently under both scenarios, with the magnitude of expansion increasing toward the end of the century and reaching 46.9% by 2100 under SSP2-4.5, likely because warming relaxed low-temperature limitation during the early seasonal transition. In contrast, suitable habitat in autumn and winter generally contracted. Autumn losses were moderate but persistent, ranging from 5.4% to 16.4%, whereas the strongest declines occurred in winter, particularly under SSP2-4.5, where habitat reductions exceeded 30% after mid-century. These contractions were likely associated with cumulative thermal stress and related environmental changes under continued warming. Summer responses were scenario-dependent, showing weak gains or net declines under SSP1-2.6 but substantial expansion under SSP2-4.5 after mid-century, reaching up to 23.6% by 2050, suggesting that habitat suitability in this season is shaped by interactions among thermal conditions, trophic support, and habitat characteristics. Overall, these findings reveal strong seasonal asymmetry in habitat responses to climate change and provide a scientific basis for seasonally adaptive management of P. trituberculatus resources in Zhoushan fishing ground.

Fishes doi: 10.3390/fishes11050259

Authors: Yukun Zhang Manabu Ishikawa Shunsuke Koshio Saichiro Yokoyama Na Jiang Weilong Wang Jiayi Chen Noman Waheed Xiaoxiao Zhang

Prophylactic antibiotic use in intensive aquaculture promotes antimicrobial resistance, necessitating the development of microbial-based interventions. This study evaluated the individual, complementary, and synergistic effects of Bacillus subtilis natto (BSN) and Lactobacillus plantarum (LP) on the physiological performance and intestinal microecology of juvenile Japanese flounder (Paralichthys olivaceus). Over a 60-day trial, juveniles (initial weight: 5.81 ± 0.03 g) received a basal diet (CON) or a diet supplemented with 107 CFU/g of BSN, LP, or both (BSN + LP). The BSN + LP consortium elicited complementary improvements in final body weight (21.39 ± 0.75 g vs. 18.66 ± 0.44 g in CON) and feed conversion efficiency (p < 0.05). Transcriptomic analysis revealed synergistic upregulation of digestive proteases (trypsin, chymotrypsin). Notably, an in pro-inflammatory markers (IL-1β, TNF-α) was counterbalanced by substantial upregulation of anti-inflammatory cytokines (IL-10, 5.65-fold; TGF-β1, 4.48-fold), suggesting the induction of mucosal tolerance rather than pathological enteritis. High-throughput 16S rRNA sequencing showed that the control cohort had a potential baseline microbial, characterized by a high relative abundance of Proteobacteria. BSN + LP administration significantly altered this microbial community into a fermentative eubiosis enriched in Firmicutes and Bacteroidota. Correlation network analyses confirmed negative interaction dynamics: increased abundance of Lactobacillus, Bacteroides, and Muribaculaceae was negatively correlated with baseline pathobiont abundance. These findings indicate that co-administration of BSN and LP hypothetically enhances metabolic energy harvest via short-chain fatty acid-producing taxa, strengthens the gut–immune axis, and competitively mitigates opportunistic pathogens.

Fishes doi: 10.3390/fishes11050258

Authors: Ling Shi Xin Shen

The high-quality development of the aquaculture industry is of great significance for ensuring food security and promoting regional economies, and improving the technological level is an important driving force for breaking through industry bottlenecks and enhancing core competitiveness. This study aims to deeply explore the multi-dimensional driving mechanism and enhancement path of aquaculture competitiveness. Based on the theoretical framework of Porter’s Diamond Model, it uses panel data from 30 provinces in the “China Fishery Statistical Yearbook” from 2014 to 2025 to empirically test the impact of technological level, resource endowment, policy support, related industries, and market scale on industry competitiveness using a partial least squares structural equation model. The empirical results show that technological level and resource endowment not only directly drive the development of supporting industries and market expansion, but also enhance overall efficiency through mediation transmission mechanisms. Policy support can stimulate market demand. Related industries play an important role in enhancing competitiveness.

Fishes doi: 10.3390/fishes11050257

Authors: Oriol Cano-Rocabayera Ysabel Santos Rosa M. Araujo Humbert Salvadó Gordon Webster Mário Pacheco Marcos Tavares-Dias Alexis Ribas Alberto Maceda-Veiga

Infectious agents shape fish populations by inducing lethal and sublethal changes that alter nutrient metabolism and metal bioaccumulation. These shifts can manifest as changes in the ionome—the specific combination of essential and non-essential chemical elements defining the whole-body composition of an individual. Understanding how pathogens shape the fish ionome is critical for developing advanced monitoring tools and clarifying the ecological roles of hosts and their pathogens. This study reports the first documented outbreak of Citrobacter freundii, Pseudomonas aeruginosa, Pseudomonas mosselii, and Shewanella xiamenensis bacterial infections in wild-caught eastern mosquitofish (Gambusia holbrooki) from three populations in Extremadura, southwestern Spain. Under laboratory-controlled conditions, we established associations between these bacterial outbreaks and the whole-fish body ionome of G. holbrooki. We compared 19 chemical elements and seven elemental ratios among diseased fish, healthy fish at the outbreak, and individuals fully recovered 100 days post-infection following antibiotic treatment. The fish ionome clearly discriminated between diseased and healthy states, and the response was consistent across all three populations. Our findings support the utility of whole-fish body elemental composition in G. holbrooki as a biomarker for environmental monitoring. Furthermore, as the bacterial infections were associated with the capture and transport-induced stress of wild individuals, this study provides critical data on the opportunistic pathogens that may be co-introduced into recipient ecosystems through the release of this widely distributed invasive fish species.

Fishes doi: 10.3390/fishes11050256

Authors: Pablo E. Picher Lorenzo Márquez Óscar Martínez Manuel Díaz

Lipolysis is an interfacial reaction. Lecithins are natural emulsifiers containing a mixture of phospholipids (PL). Lecithin composition can be modified via enzymatic hydrolysis of PLs to produce lysophospholipids (LPL). The quantities of PL and LPL and the PL/LPL ratio are related to the emulsifying properties and interfacial activity of digestive lipases. This study aims to: (i) produce oil-in-water nanoemulsions of rapeseed oil (RSO) with soybean lecithin (SBL) and hydrolyzed lecithin (HL) at different concentrations and homogenization pressures and measure the mean droplet diameter (MDD) and polydispersity index (PdI) by dynamic light scattering; (ii) hydrolyze the emulsions in vitro with intestinal extracts of rainbow trout and estimate the degree of hydrolysis of lipids (DH) by the pH-stat method; and (iii) model the results on MDD, PdI, and DH through the response surface methodology (RSM). When HL was used as an emulsifier, DH, MDD, and PdI were fitted to polynomial quadratic, two-factor interaction, and linear models, respectively. MDD, PdI, and DH were fitted to polynomial quadratic SBL models. The optimal conditions were emulsifier concentrations of 0.45% and 0.76% w/w and homogenization pressures of 10,790 and 10,781 psi for HL and SBL, respectively. Under these conditions, DH = 34.9% and 33.08%, MDD = 241.9 and 543.6 nm, and PdI = 0.29 and 0.52 for HL and SBL, respectively.

Fishes doi: 10.3390/fishes11050255

Authors: Victor Niță Leonardo Aguiari Carmen Georgeta Nicolae Daniela Roșioru Aurelia Ţoţoiu Magda Nenciu

Oyster aquaculture offers promising opportunities for diversifying marine production in the Romanian Black Sea, where favorable environmental conditions and recent regulatory developments support shellfish farming. This study aimed to generate baseline data for the cultivation of the Pacific oyster, Magallana gigas, through an in situ experimental trial conducted off Mamaia Bay, Romania. A 50 m experimental long-line system was deployed at 13.5 m depth, and triploid oysters were cultured for one year at two depth horizons (3 m and 6 m). The growth performance, meat yield, Condition Index, microbiological quality, environmental parameters, and epibiotic communities were monitored monthly. Cultivation depth significantly influenced oyster growth, with individuals reared at 6 m consistently achieving a greater wet weight and shell length than those at 3 m. Growth rates peaked during spring, and meat yield values indicated good commercial quality. Environmental monitoring showed strong seasonal variability, with high summer temperatures and reduced dissolved oxygen associated with increased mortality. Microbiological analyses revealed higher bacterial loads during warm months. The Condition Index classified the oysters as generally “fine” to occasionally “special”. Overall, the results demonstrate that Black Sea conditions can support successful cultivation of M. gigas, although seasonal environmental stress and epibiosis require appropriate farm management.

Fishes doi: 10.3390/fishes11050254

Authors: Aldo Fraijo-Valenzuela Joe Luis Arias-Moscoso Francisco Cadena-Cadena Barbara Aboites-Martínez Ramón Casillas-Hernández Libia Zulema Rodriguez-Anaya Pablo Gortáres-Moroyoqui Jose Reyes Gonzalez-Galaviz

A 10-week feeding experiment was conducted to evaluate the effects of replacing fishmeal with cricket meal on the productive performance and transcriptional responses of genes related to nutrient metabolism and growth of blue tilapia (Oreochromis aureus). Five conventional tilapia feeds were formulated to replace fishmeal with cricket meal. Control diet (CD) was formulated with 20% fishmeal, and four diets gradually replaced fishmeal with cricket meal at 20, 40, 60, and 80% (D1–D4). A total of 200 fingerling tilapia (2.00 ± 0.09 g) were randomly distributed into 20 tanks (10 fish/tank), with four replicates per dietary treatment. The results showed that fish fed CD and D1 had higher growth performance values than those fed D2–D4. The feed conversion ratio (FCR) was significantly better in fish fed CD and D1 compared with fish fed D2–D4. The survival rate was similar for all treatments. The transcriptional response of genes related to nutrient digestion, absorption, and transport; lipid metabolism; and the somatotropic axis was marked downregulated in fish fed D2 and D4, whereas in fish fed D3, it exhibited a unique compensatory regulation across most pathways, likely sustained by its higher dietary lipid content. Although cricket meal did not prevent the metabolic effects associated with high soybean meal inclusion, survival remained high across all treatments. Cricket meal can replace up to 20% of the fishmeal in the feed for blue tilapia fingerlings, with soybean meal as the main protein source.

Fishes doi: 10.3390/fishes11040253

Authors: Suhaila Karim Khalil Jaser Caio Augusto Perazza Rodrigo Rodrigues Domingues Freddy Arocha Eric Hallerman Alexandre Wagner Silva Hilsdorf

Populations of several billfish species are declining due to overfishing and bycatch, and fundamental aspects of their biology and population dynamics remain poorly understood. We provide the first assessment of the population genetic structure of longbill spearfish (Tetrapturus pfluegeri) in the western Atlantic Ocean. We screened variation at 12 nuclear microsatellite loci (n = 144) and mitochondrial DNA control region sequences (mtCR, n = 177). Both marker types revealed three genetically differentiated clusters, with mean values for microsatellites showing differentiation of FST = 0.136 and DEST = 0.201, and for mtCR FST = 0.645. Microsatellite markers demonstrated moderate-to-high genetic diversity, with a mean allelic richness of 6.73 alleles per locus, moderate heterozygosities (Ho = 0.446, He = 0.604), and a positive inbreeding coefficient (FIS = 0.22) across the three sample collection sites. The overall estimated effective population size was 789.2 (95% CI: 246.7–∞). The mtCR exhibited 96 haplotypes, with high haplotype (0.989 ± 0.003) and nucleotide (0.025 ± 1.3%) diversities. We found higher mean relatedness within clusters than among them, supporting the interpretation of population subdivision and the Wahlund effect. Tajima’s D and Fu’s Fs were negative across all localities, with significant values observed along the Brazilian coast but not in the Caribbean Sea. These neutrality test results, together with low Harpending’s raggedness indices from DNA sequence mismatch distributions, are consistent with historical demographic expansion. Our findings establish a genetic baseline for fishery monitoring and management, contributing to the conservation of T. pfluegeri populations in the western Atlantic Ocean.

Fishes doi: 10.3390/fishes11040252

Authors: Nguyen Duc Minh Nguyen Thanh Trung Ly Tuan Kiet Truong Van Than Nguyen Ngoc Ha Pham Ngoc Hoang Vo Thi Kim Chi Nguyen Minh Thanh Nguyen Phuc Cam Tu

Monosex all-male culture of the giant freshwater prawn (Macrobrachium rosenbergii) maximizes aquaculture yield due to a male growth advantage, but direct hormonal treatment of grow-out populations poses significant food safety risks. This study evaluated the efficacy of dietary 17β-estradiol (E2) in inducing functional neo-females from a fully all-male postlarval population to support an indirect monosex seed production strategy. All-male postlarvae were fed diets supplemented with E2 at concentrations of 0, 50, 100, 150, and 200 mg/kg for 36 days, followed by a 150-day hormone-free post-treatment period to assess growth performance, feminization rates, and gonadal histology. E2 administration successfully induced feminization across all treatments, reaching a peak rate of 35.5% at 150 mg/kg, whereas the control group remained entirely male. During the 36-day treatment period, E2 supplementation transiently enhanced specific growth and survival rates but concurrently reduced feed conversion ratios. Notably, these physiological differences disappeared completely over the 150-day post-treatment phase. Histological assessments confirmed that E2-induced neo-females exhibited normal oogenesis, with gonadosomatic index (GSI) values and oocyte diameters similar to those of wild-caught females. This establishes a definitive, physiologically safe, and non-surgical protocol for producing the neo-female broodstock necessary to sustain high-yield commercial monosex populations.

Fishes doi: 10.3390/fishes11040251

Authors: Aris Widagdo Gun-Ho Lee Subong Park

This study presents a comparative evaluation of the sinking performance of traditional small-scale purse-seine gears used in Aceh and Papua, Indonesia, using a three-dimensional mass–spring framework validated by sea-trial data from the Java Sea. Simulations compared sinking behavior under changes in the netting material, knot type, mesh size, and total sinking force across region-specific gear configurations. Compared with existing gear configurations, both modified gear scenarios demonstrated improved sinking performance in Aceh and Papua. In Aceh, the average sinking speed increased from 0.07 to 0.15 m/s in Improved Gear I and to 0.18 m/s in Improved Gear II, while the maximum depth increased from 37.3 to 54.8 m and 56.2 m, respectively. In Papua, the average sinking speed increased from 0.08 to 0.18 m/s and 0.20 m/s, while the maximum depth increased from 37.2 to 56.8 m and 60.6 m, respectively. In both regions, Improved Gear II exhibited the highest sinking performance. Enhanced sinking performance was accompanied by higher purse-line tension during pursing, with maximum values of 1666 kgf in Aceh and 1589 kgf in Papua. These results suggest that design tendencies identified in previous Indonesian studies, particularly a comparative reference sinking force (1.24 kgf/m), larger mesh size, and knotless polyester netting, appear consistent across the two regional cases examined. However, because the modified scenarios represent coupled multivariable scenarios and direct local field validation was not available for Aceh and Papua, the findings should be interpreted as comparative simulation-based evidence for assessing gear-modification options rather than as absolute in situ predictions.

Fishes doi: 10.3390/fishes11040250

Authors: In Joon Hwang Jong Cheol Han

Silver pomfret (Pampus argenteus, family Stromateidae) is a highly valuable marine fish species with significant commercial demand; however, its aquaculture remains undeveloped due to limited knowledge of captive breeding and seed production. To our knowledge, this is the first successful report on the induction of maturation, natural spawning, and larval rearing of silver pomfret under captive conditions in Korea. Wild broodstock (33 individuals in 2020; 250 individuals in 2021) were collected from the southern coastal waters of Korea using set nets. In the first year, water temperature management alone successfully induced gonadal maturation, as evidenced by a significant increase in the gonadosomatic index (GSI) and the presence of vitellogenic oocytes (400–500 μm) in April. In the second year, natural spawning was observed on fifteen occasions from May to September 2022, yielding a total number of 157,050 eggs. Fertilized eggs were spherical, transparent, and pelagic, with diameters ranging from 1.29 to 1.37 mm. Hatched larvae (total length: 4.85 ± 0.22 mm) exhibited poor feeding responses to rotifers and high early mortality within two weeks post-hatching, with the maximum rearing period reaching 24 days post-hatching. These findings demonstrate that water temperature management alone is sufficient to induce maturation and natural spawning of silver pomfret, and highlight the critical need for optimizing larval feeds, improving broodstock nutritional management, and conducting endocrine profiling during reproduction to establish a complete aquaculture protocol for this species.

Fishes doi: 10.3390/fishes11040249

Authors: Zukun Wu Kun Ding Yuxuan Bao Peng Zhang Xinyue Ma Maolin Hu Shengfu Zhou

To understand the distribution characteristics of the fish community and evaluate the effectiveness of the Yangtze River fishing ban, this study selected the Fuhe River (an important tributary of the Yangtze River) as the research area. A total of 30,892 fish (belonging to seven orders, 20 families, and 92 species) were captured in the upper and middle reaches of the Fuhe River from 2022 to 2024. Among them, the Cypriniformes order accounted for the largest proportion, with nine families and 66 species, making up 71.74% of the total number of fish. According to the relative importance index, Carassius auratus was the dominant species for each sampling period and each sampling area. Moreover, the number of dominant species in the main streams was significantly higher than that in the tributaries, while the diversity of the fish community in the tributaries was significantly greater than that in the main streams. Additionally, ANOSIM revealed significant spatial differences in the fish community (p < 0.01). Cluster and NMDS analyses further divided the fish community into three groups. SIMPER indicated that the typical species of each group of fish community were basically the dominant species within that community. Furthermore, RDA indicated that potassium permanganate, ammonia nitrogen, total phosphorus, and chlorophyll a were the main water environmental factors affecting the fish community structure. Compared to the fish community before the fishing ban, the stability of the fish communities during the initial stage of the fishing ban was significantly improved, and the number of fish species also increased. Therefore, the fishing ban was beneficial for enhancing the diversity and stability of the fish community. However, compared with the composition of fish species before the fishing ban, a certain number of fish species in the upper and middle reaches of the Fuhe River were still not collected during the early stage of the fishing ban. Therefore, the ten-year fishing ban in the Yangtze River still needs to be continued and implemented.

Fishes doi: 10.3390/fishes11040248

Authors: Guangbao Zhang Abdulai Merry Kamara Zhijie Zhou Wenbin Chen Yang Jie Chaoshu Zeng Wenquan Zhou Xugan Wu

Monosex culture has been shown to enhance farming productivity in several decapod crustaceans, and it has also been suggested that this approach holds high potential for the sustainable aquaculture of the Chinese mitten crab, Eriocheir sinensis. Pronounced sexual dimorphism in E. sinensis facilitates the implementation of a monosex culture. This study aimed to compare the growth, gonadal development, culture performance, and economic outcomes of two monosex culture modes, i.e., an all-female culture and an all-male culture, as well as a mixed-sex culture (males: females = 1:1) during an 8-month growth period in earthen ponds. The results showed that: (1) Throughout the grow-out period, the average body weight in both monosex culture treatments was consistently higher than in the mixed-sex treatment, with a significantly greater body weight in the all-female and all-male treatments than that of males and females in the mixed-sex treatment being detected during mid-June and October, respectively (p < 0.05). (2) The percentages of both sexes that had finished puberty molting were mostly similar between the monosex and mixed-sex treatments between July 20th to October 10th, although the all-female treatment had a significantly lower puberty molting percentage than the mixed-sex treatment on August 10th (p < 0.05). Gonadosomatic index (GSI) values were similar between the monosex and mixed-sex treatments for both males and females (p > 0.05). (3) At harvest period, the final body weight in the all-male treatment was significantly higher than that of the mixed-sex treatment (p < 0.05). In contrast, the all-female treatment exhibited a significantly higher survival rate and a lower limb injury rate compared with the mixed-sex treatment (p < 0.05). As a result, the yield of the all-male and all-female treatments exceeded that of the males and females in the mixed-sex treatment by 24% and 13%, respectively. Additionally, the mixed-sex treatment also had a significantly higher feed conversion ratio (p < 0.05). Finally, the monosex treatments had a higher proportion of large crabs (males ≥ 200 g, females ≥ 175 g) and a lower proportion of small crabs (males ≤ 150 g, females ≤ 100 g) compared to the mixed-sex treatment. (4) In terms of economic benefits, net profit and return on investment (ROI) were highest under the all-female treatment, while the mixed-sex treatment recorded the lowest total return, net profit, and ROI (p < 0.05). In conclusion, an all-female culture is recommended for the grow-out culture period of E. sinensis, as it led to a higher survival rate, produced larger-sized crabs and generated greater overall economic benefit.

Fishes doi: 10.3390/fishes11040247

Authors: Marina Paixão Gil Mario Vinicius Condini Maurício Hostim-Silva Felippe Alexandre Daros

Understanding habitat use and connectivity in estuarine fishes is essential for effective conservation and management. In this study, otolith microchemistry was applied to investigate habitat use and connectivity of the estuarine catfish Genidens genidens across three estuaries in southeastern Brazil. A total of 58 individuals were analyzed using laser ablation inductively coupled plasma mass spectrometry, focusing on strontium-to-calcium (Sr:Ca) and barium-to-calcium (Ba:Ca) ratios. Variations in elemental ratios along otolith transects were used to infer individual ontogenetic patterns along the estuarine–marine gradient. Most individuals exhibited combined use of estuarine and marine environments, while trajectories restricted to freshwater were rare. The apparent complexity of chemical profiles tended to increase with age; however, this pattern disappeared after correction for size-related bias, suggesting that age itself did not significantly influence habitat-use transitions. These patterns are consistent with ecological plasticity and partial migration within populations of G. genidens, although they may also reflect exposure to variable environmental conditions. Sr:Ca ratios were useful indicators of salinity-related transitions, whereas Ba:Ca ratios provided complementary information associated with continental influence. Overall, this study highlights the applicability of otolith microchemistry for investigating habitat-use patterns in estuarine fishes and reinforces the ecological importance of estuaries for feeding, growth, and recruitment in G. genidens, while acknowledging inherent limitations related to environmental variability and proxy interpretation.

Fishes doi: 10.3390/fishes11040246

Authors: Chengxu Ruan Junhao Tang Xiufang Liu Junwei Chen Linxi Cheng Xucong Lv

This study compared the effects of dietary Lactobacillus plantarum (Lpl) and selenium-enriched L. plantarum (Lpl_se) on the growth, hepatic antioxidant capacity, and intestinal microbiota of juvenile largemouth bass (initial weight 12.50 ± 0.81 g). Following a 58-day trial in an indoor rearing system, data were analyzed using one-way ANOVA followed by Tukey’s HSD test. Results showed that both Lpl and Lpl_se significantly improved growth versus the control (Weight Gain Rate: 379.82% and 387.18% vs. 326.56%; p < 0.05). Both supplements significantly elevated hepatic antioxidant enzymes (SOD, CAT, GSH) and reduced malondialdehyde (MDA) levels (p < 0.05). Notably, these macroscopic parameters showed no statistical differences between the two probiotic treatments. However, 16S rRNA sequencing revealed distinct metabolic strategies. While both treatments enriched intestinal Lactobacillus, Lpl_se uniquely upregulated energy-harvesting and synthetic pathways (glycolysis and lysine biosynthesis), corroborated by increased intestinal glycogen synthase activity. In conclusion, while selenium enrichment did not further improve macroscopic growth statistically, it differentially modulated the intestinal functional profile towards enhanced carbohydrate and amino acid metabolism, presenting an alternative host nutrient assimilation strategy.

Fishes doi: 10.3390/fishes11040245

Authors: Hongyu Xie Yong Liu Jinhui Sun Jianzhong Shen Teng Wang

Against the backdrop of global coral reef degradation, benthic resource structure is shifting from coral dominance to turf algae and detritus-dominated epilithic algal matrix (EAM). As a typical detritivorous reef fish, Ctenochaetus striatus (Quoy & Gaimard, 1825) plays an important ecological role in regulating the functioning of degraded coral reef ecosystems. Using stable isotope analysis (δ13C and δ15N), this study systematically compared the trophic niche characteristics of different size classes of C. striatus across four reef habitats in the Xisha Islands, South China Sea, representing a gradient of disturbance (Qilianyu Island > Lingyang Reef > North Reef > Langhua Reef), in order to elucidate habitat-specific ontogenetic shifts and their adaptive features. The results showed that C. striatus from Qilianyu Island and Lingyang Reef exhibited overall higher δ15N values, suggesting an overall pattern consistent with stronger nitrogen enrichment at the more disturbed reefs, whereas individuals from Langhua Reef had significantly lower δ13C values, indicating a stronger reliance on offshore-derived carbon pathways. Across size classes, the trophic niche area (SEAc) and intraspecific trophic heterogeneity, measured as mean nearest neighbor distance and standard deviation of nearest neighbor distance, of populations from Qilianyu Island, Lingyang Reef, and North Reef generally decreased with increasing body size, revealing a pattern of trophic convergence toward core resources. In contrast, the Langhua Reef population exhibited a distinct expansion–contraction pattern, suggesting flexible resource use across developmental stages under conditions of low human disturbance and high resource heterogeneity. Although smaller size classes generally showed high probabilities of niche overlap among reefs, overlap declined markedly in the largest size class, with most values falling below 50%, indicating that resource assimilation strategies increasingly reflected reef-specific resource backgrounds. These findings demonstrate that ontogenetic trophic niche shifts in C. striatus are not fixed, but are highly dependent on local resource context and habitat conditions. In degraded reefs with simplified resource structure, individuals tend to converge on core resource spectra to maintain survival, whereas in healthier reefs with greater habitat heterogeneity, they tend to show greater variation in major food sources and resource use. This study provides a theoretical basis for coral reef ecological restoration.

Fishes doi: 10.3390/fishes11040244

Authors: Phillip Dettleff Marcia Arriagada-Solimano Vania Fuentealba Karina Tobar Millaray Sáez Claudio Olave Juan Manuel Estrada Juan Antonio Valdés

The red cusk-eel (Genypterus chilensis) is an endemic Chilean teleost fish of significant importance to fisheries and aquaculture; however, no reference genome is available for this species. In this study, we present the first hybrid genome assembly of G. chilensis using Nanopore long-reads and Illumina short-reads, integrated with structural and functional annotations from RNA-seq data of the intestine and head kidney. The resulting genome assembly was 439.89 Mb in size, with an N50 of 7.96 Mb, containing 35,029 coding genes. Comparative genomics with G. blacodes revealed high similarity in genome size and completeness. Additionally, 14,681 lncRNAs were annotated, with 641 lncRNAs and 7323 coding genes differentially expressed in a tissue-specific expression pattern. These findings provide a high-quality genomic resource that enhances the understanding of lncRNA regulation and genome structure in the Genypterus genus. This study establishes a foundation for future research on commercial traits, conservation, and the evolution of the Ophidiiformes order.

Fishes doi: 10.3390/fishes11040243

Authors: Tingting Wen Hongwu Cui Zhengguo Cui Xinxing Zhang Qi Zhang Juanjuan Sui Xixi Han Huanhuan Jiang Congcong Xing Mian Xie Yanrong Zhou Weihan Yin Shengtao Chen Qian Yang

To evaluate the potential biological effects of electromagnetic fields from offshore wind farms on Sebastes schlegelii, a laboratory-controlled chronic exposure experiment was conducted using a magnet-based static magnetic field system. Each group contained 60 fish distributed across four replicate tanks, with 15 fish per tank, and the fish were continuously exposed for 20 d under controlled water-quality conditions. Daily video monitoring of collective shoaling behavior was combined with multi-tissue physiological and biochemical analyses. Electromagnetic field exposure increased the swimming speed, burst frequency, activity ratio, spatial coverage, occupancy entropy, and polarization, while reducing the nearest neighbor distance, group radius, and group area. At the physiological level, cortisol increased mainly in the liver and brain, ACTH showed tissue-dependent modulation, SOD remained relatively stable, and glutathione increased in multiple tissues, especially in the liver, gut, and brain. Correlation analysis indicated a close coupling between behavioral reorganization and endocrine–redox regulation, suggesting that chronic EMF exposure shifted Sebastes schlegelii into a stress-associated but functionally coordinated collective state.

Fishes doi: 10.3390/fishes11040242

Authors: Yue Tan Yang Xu Li Jia Youqin Kong Zhili Ding Changle Qi Qiyou Xu

To investigate the effects of three alternative protein sources—Hermetia illucens larvae meal (HIM), Chlorella meal (CM) and stickwater meal (SWM)—on the vitellogenin in female largemouth bass (Micropterus salmoides), these protein sources were used to replace 0% (control group, FM; containing 40% fishmeal), 25% and 50% of the fishmeal in the diet. A total of seven isonitrogenous and isolipidic diets were formulated (FM, 25% HIM, 50% HIM, 25% CM, 50% CM, 25% SWM and 50% SWM). The healthy female fish with an initial body weight of 353.57 ± 28.12 g were fed the experimental diets for eight weeks. The results showed that the viscerosomatic index, gonadosomatic index and oocyte diameter of broodstock in the 50% HIM group were significantly higher than those in the FM group. The 50% HIM group showed the highest rate of stage IV oocytes and the lowest share of stage II oocytes. Hepatic vitellogenin (Vg) mRNA expression was significantly upregulated in the 50% HIM group, whereas ovarian mRNA expression of Vg and vitellogenin receptor (VgR) was significantly upregulated in the 25% SWM and 50% SWM groups. In conclusion, replacing 50% of dietary fishmeal with Hermetia illucens larvae meal can promote ovarian development in largemouth bass broodstock by increasing the gonadosomatic index and the expression of genes involved in vitellogenin synthesis.

Fishes doi: 10.3390/fishes11040241

Authors: Jiaxin Liu Hui Tang Yirong Li Haiyang Yu Jianguang Cai Chongqing Wang

Skeletal muscle activity, such as exercise, enhances mitochondrial function, a process critical for ATP production through oxidative phosphorylation. Mitochondrial dysfunction, often linked to mutations in the chchd10 gene, contributes to the pathogenesis of neurodegenerative and neuromuscular diseases. Although exercise is known to improve mitochondrial performance, its regulatory influence on chchd10 remains poorly defined. In this study, zebrafish (Danio rerio) at three different ages (4, 9, and 15 months) were divided into control and exercise groups, with the latter subjected to a swimming intervention. We observed that exercised male zebrafish exhibited improved muscle morphology across all age groups, marked by increased muscle fiber cross-sectional area and reduced inter-fiber spacing. Transcriptome sequencing via RNA-seq further identified chchd10 as a differentially expressed gene in three age group comparisons. Exercise may be associated with downward regulation of expression of chchd10, which was correlated with increased methylation levels in its promoter region. These results illuminate the epigenetic mechanisms induced by exercise, revealing a novel pathway through which physical activity, potentially via modulation of chchd10, promotes muscle and mitochondrial health.

Fishes doi: 10.3390/fishes11040240

Authors: Qiang Ma Houguo Xu

With the rapid expansion of global aquaculture, the stagnating production and fluctuating prices of fishmeal and fish oil have become limiting factors for the sustainable development of the aquafeed industry [...]

Fishes doi: 10.3390/fishes11040239

Authors: Aiman Nadeem Farkhanda Asad Asma Ashraf Tayyaba Ali

Feed nutrition and rise in antibiotic resistance are growing global challenges in aquaculture, with Aeromonas hydrophila causing significant losses in the carp family. This 60-day study evaluated the potential of combining herbal seed extract (Achyranthes aspera and Ricinus communis) with inactivated vaccine (A. hydrophila) to enhance growth and immunity in Labeo rohita. A total of 540 fish were randomly assigned in six groups (T0-untreated control, T1-A. aspera seed extract (ASE), T2-R. communis seed extract (RSE), T3-vaccinated control, T4-vaccine plus ASE, T5-vaccine plus RSE). Results revealed that herbal–vaccine combinations, particularly T4, showed highest growth performance (p < 0.05). Furthermore, this group showed improved metabolic profiles, indicated by reduced serum cholesterol, triglycerides, and glucose, along with significantly elevated albumin and globulin concentrations. In terms of immune response, neutrophil counts were significantly higher in T4 and T5. Crucially, following a challenge with A. hydrophila, survival rates were higher in T4:90% and T5:85% compared with positive control’s meager 20% survival. Post-challenge hematology confirmed that groups T4 and T5 maintained an enhanced immune status. These findings suggest that combining medicinal plants extract with vaccine effectively enhances growth, immunity, and disease resistance in L. rohita, presenting an environment friendly alternative to traditional antibiotics in aquaculture.

Fishes doi: 10.3390/fishes11040238

Authors: Rinat Barakov Nina Badryzlova Saule Assylbekova Naila Bulavina Farizat Altayeva Almat Suyubaev Moldir Aubakirova

This study provides a comparative analysis of phenotypic variability in the morphological traits of tench (Tinca tinca L.) reared under aquaculture conditions and those from a natural population in southern Kazakhstan. The aim of the study was to evaluate phenotypic plasticity and adaptive differentiation between populations shaped by contrasting ecological and trophic environments. Morphometric analysis revealed significant differences in indices associated with growth patterns and body shape. The aquaculture group demonstrated faster somatic growth and lower variability, whereas the wild population exhibited greater morphological diversity, likely reflecting the effects of natural selection and habitat heterogeneity. The results indicate pronounced phenotypic divergence between pond-reared and wild tench, which is likely driven by environmental conditions and aquaculture practices. These findings highlight the high adaptive plasticity of the species and support its potential for domestication and large-scale aquaculture in Kazakhstan. Overall, the data may contribute to the development of conservation and restocking programs for natural populations, as well as to selective breeding strategies and sustainable aquaculture practices.

Fishes doi: 10.3390/fishes11040237

Authors: Erimi Kendrick Nadya Mamoozadeh William G. Cope Russell Borski Robert W. Clark Michael S. Hopper Benjamin J. Reading

Reliable developmental benchmarks are essential for synchronizing incubation and first-feeding decisions in striped bass (Morone saxatilis) hatcheries, yet existing references are incomplete, outdated, or difficult to apply across variable temperature regimes. We developed contemporary embryo and larval developmental staging guides for striped bass using digital imaging and degree day standardization and paired these guides with measurements of early larval mortality and endogenous energy depletion to provide practical context for hatchery management. Larvae were photographed from hatch through metamorphosis to document key morphological transitions, including yolk absorption, mouth formation, swim bladder inflation, fin differentiation, pigmentation, and diet-related developmental milestones. To place these stages in physiological and survival context, aquarium trials showed there was no clear density-dependent mortality across rearing densities of 1.1–6.8 larvae/mL within the first 72 h post-hatch. Yolk reserves were typically depleted by approximately 4–6 days post-hatch (dph), while lipid droplets persisted longer as secondary endogenous energy stores in unfed larvae through 15 dph. Together, these staging guides provide a transferable developmental framework from fertilization to metamorphosis that links external morphology to endogenous reserve depletion and first feeding, thus supporting standardized hatchery monitoring, improved feeding synchronization, and more consistent assessment of embryo and larval quality.

Fishes doi: 10.3390/fishes11040236

Authors: Wei Shen Zhaowei Yin Bao Zhang Lekang Li Enze Qian Xiaoling Gong

To scientifically assess the fish resource status and spatial distribution in the Huoyanshan waters of Poyang Lake for the conservation of endangered species like Coilia nasus, an acoustic survey was conducted using a dual-frequency identification sonar (DIDSON) in July 2024. Fish targets were identified and extracted by combining an Echoview-based identification and deep learning models. Catch statistics were integrated to estimate fish density, abundance, biomass, and spatial distribution patterns. A total of 1891 fish targets were detected. The Echoview model achieved an average accuracy of 90.83%, while the YOLO model attained average precision and recall of 0.941 and 0.869, and the DeepSORT model attained precision and recall of 0.887 and 0.911. The total fish abundance was estimated at approximately 223,775 individuals, with a total biomass of about 199,742 kg. Spatially, fish were predominantly distributed in nearshore areas horizontally and concentrated at depths of 5–15 m vertically. The integrated approach combining DIDSON, Echoview and deep learning models proved effective for high-accuracy fish target identification and resource estimation, with deep learning models offering greater objectivity and processing efficiency. This study provides a technical reference for intelligent fish target identification in sonar images and provides baseline data and a technical reference for subsequent fish resource monitoring and management in the Huoyanshan waters of Poyang Lake.

Fishes doi: 10.3390/fishes11040235

Authors: Fátima Adrio Xoana Taboada Paulino Martínez Ana Viñas

Genes involved in sexual development have been identified in many teleost fishes, including the turbot, a flatfish of high commercial value in aquaculture. In this species, a major sex determination (SD) Quantitative Trait Locus has been identified, and Sox2 has been proposed as the SD gene. Although RT-PCR, qPCR, and transcriptomic analyses have been performed on turbot gonads, histological studies remain limited. Here, we examined the tissue-specific expression patterns of several sex-related genes in turbot using in situ hybridization on paraffin sections (SISH) of differentiated ovaries and testes of juvenile and adult specimens. Vasa, Foxl2, Amh, Sox2 and Sox17 transcripts were detected in both male and female gonads, whereas Cyp19a1a and Sox19 expression was restricted to the ovary; these results support previous gene expression analyses and suggest a role for these genes in gonadal development and reproductive functions in this species. SISH provides complementary information to molecular analyses by identifying the specific cell types expressing the sex-related genes analyzed in gonadal tissue, thereby offering a more comprehensive understanding of gonadal differentiation in turbot. Comparison with results reported for the gonads of other teleost species revealed similar tissue-specific gene expression patterns during sexual development.

Fishes doi: 10.3390/fishes11040234

Authors: Phan Trong Binh Satoshi Hori Nguyen Thi Dang Katsuhisa Uchida Yousuke Taoka

We evaluated the effect of our light-emitting diode (LED) light treatments (blue, peak at 468 nm; green, peak at 537 nm; red, peak at 630 nm; and white light) on the growth performance and serum lysozyme activity of the common carp Cyprinus carpio and bacterial communities in a closed recirculating system under an average power intensity of 1.29 ± 0.18 mW/cm2 of LED light on the water surface of a circulating rearing system for 70 days. The specific growth rate, weight gain and K-factor were improved when carp were cultured under green or blue light. The specific lysozyme activity in the plasma of the common carp was significantly promoted under blue light compared to the green, white and red light conditions after 70 days. Compared to the other types of LED lights, the blue light treatment resulted in the lowest number of heterotrophic bacteria in the rearing water and the highest heterotrophic bacteria in the carp’s gut contents (both p < 0.05). The phyla Fusobacteria, Bacteroidetes, Tenericutes, Proteobacteria and Firmicutes were abundant in the carp’s gut contents after culturing with any of the four types of LED light. In short, the blue LED light can be considered a potential tool in sustainable aquaculture.

Fishes doi: 10.3390/fishes11040233

Authors: Zhong Tang Xinxin Yu Xin Chen Junwen Liang Yangyang Tu Zhifeng Zhou Faxian Yu Chun Zhang Siyu Fan Min Tao

The diploid distant hybrid (2nBY) derived from female blunt snout bream (Megalobrama amblycephal, BSB) × male Bleeker’s yellow tail (Xenocypris davidi Bleeker, YT). To investigate the hypoxia tolerance and the regulatory mechanisms of hypoxia-inducible factor-1α/2α (hif-1α/2α) in 2nBY, BSB, and YT, experiments consisting of 24 h of hypoxia treatment (DO = 2.0 ± 0.1 mg/L) followed by 6 h of reoxygenation were conducted. The loss of equilibrium critical oxygen pressure (LOEcrit), gill tissue structure, and antioxidant indices, as well as the full-length sequences and expression of hif-1α/2α in 2nBY, BSB, and YT, were compared. The results showed that the LOEcrit value of 2nBY was significantly lower than that of BSB but higher than that of YT (p < 0.05). After hypoxia treatment, the changes in gill tissue structure and antioxidant indices of 2nBY were less obvious than those of BSB, and the recovery rate was faster after reoxygenation. Sequence analysis revealed high similarity of hif-1α/2α between YT and 2nBY. After hypoxia treatment, hif-1α/2α were upregulated in the liver but showed distinct gill expression among the three groups. Their gill expression differences may contribute to varied hypoxic tolerance. Distant hybridization between BSB and YT successfully generated hybrid offspring with enhanced hypoxia tolerance relative to BSB. These results provide theoretical and technical support for the breeding of a new hypoxia-tolerant germplasm resource of bream.

Fishes doi: 10.3390/fishes11040232

Authors: Shunxiang Yang Yingli Zhang Zefang Liao Dengke Cao

Global warming presents urgent challenges for tilapia aquaculture. This study introduces a tailored loss function to assess long-term impacts under extreme drought, using historical drought data in China as a baseline. The TaiESM1 climate model within the CMIP6 framework is applied to project future conditions under SSP245, SSP370, and SSP585 scenarios, focusing on Guangdong Province (2024–2100). The results indicate a general decline in the frequency of extreme droughts across all scenarios. Under SSP245, technological advancements combined with reduced drought risk may boost yields of tilapia aquaculture of Guangdong to 2.369–2.418 million tons by 2100. In SSP370 and SSP585, while humidity increases, drought risk reduction is less pronounced, resulting in marginally lower yields (2.285–2.408 and 2.300–2.416 million tons, respectively). When a unified loss parameter is applied, projected yields exhibit a U-shaped trend across all SSP scenarios, reaching a minimum under SSP370 in the mid-century period before recovering toward the end of the century, driven by scenario-dependent marginal responses of production to changes in extreme drought risk, highlighting the nonlinearity of climate impacts driven by complex climatic factors and socioeconomic interactions. These findings are subject to uncertainties associated with the use of a single climate model and the simplified representation of drought impacts in the loss-function framework.

Fishes doi: 10.3390/fishes11040231

Authors: Qinlang Liang Yazhi Luan Zhengwen Wang Jiangbo Niu Yasong Li Hua Tang Zengting Li Songming Zhu Gang Liu

Songming Zhu was not included as an author in the original publication [...]

Fishes doi: 10.3390/fishes11040230

Authors: Zuzy Anna Asep A. Handaka Lantun P. Dewanti Nurani Khoerunnisa Syawaluddin A. Harahap Jogi R. N. Panggabean Yeni Mulyani Donny J. Prihadi Helmalia Asri Bagus D. Cahyo Ripky Alfareza Muhammad S. A. Mubarok Noir P. Purba

Small-scale fisheries constitute the backbone of coastal livelihoods in Indonesia, yet comprehensive socio-economic data remain limited for effective management. This study characterizes the operational and socioeconomic patterns of multi-gear artisanal fisheries in the Pangandaran coastal waters of West Java, Indonesia. A cross-sectional survey of 136 fishers across 14 coastal communities was conducted using structured questionnaires covering socio-demographic characteristics, fishing operations, and catch composition. Complete economic data were available for 125 fishermen, while multivariate analyses used n = 105 due to listwise deletion of cases with missing predictor variables. Fishermen averaged 46.9 years of age with 25.8 ± 11.6 years of fishing experience. Mean monthly income was IDR 5.80 million (SD = 7.51, 95% CI: 4.47–7.13 million, approximately USD 387). Gillnet was the dominant fishing gear (73.5% of fishermen), followed by hook-and-line (14.7%). A total of 57 fish species were recorded, dominated by hairtail Trichiurus spp. (61.0% occurrence). Statistical analyses revealed weak relationships between conventional demographic and operational variables and income. Although crew number showed a statistically significant association with income (p = 0.039), its effect size was small, and the overall regression model was not significant, with very low explanatory power (R2 = 0.038). These results indicate that income variability is largely driven by unmeasured and context-specific factors rather than observable fishing characteristics. These findings provide baseline socio-economic data essential for developing community-specific management interventions in Pangandaran waters.

Fishes doi: 10.3390/fishes11040229

Authors: Bo Zhu Juan Feng Dong Qian Ping Zhuang Changkao Mu Jiong Chen Rongrong Ma

Enterocytozoon hepatopenaei (EHP) is a specialized parasitic microsporidian that causes significant economic losses to the shrimp farming industry. The glycolysis pathway plays an important role in the survival of EHP spores in vitro. In this study, key enzyme genes involved in the glycolysis pathway of EHP were analyzed, and purified spores were treated with KOH and a low temperature (−20 °C) to promote or inhibit germination. Quantitative analysis and enzyme activity of the initiating key gene hexokinase (HK) and the core link gene glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were conducted to explore the energy response characteristics of germinating spores. The results showed that HK and GAPDH genes had significant differences from the host, based on phylogenetic analysis. The expression of HK gene and enzyme activity increased after promoting germination treatment. The expression of the GAPDH gene was stable, but the activity of the GAPDH enzyme increased significantly after germination promotion. These findings indicate that the inhibition of the HK gene expression level and GAPDH protein level can block spore germination and invasion in vitro, which could be used as potential control targets for EHP.

Fishes doi: 10.3390/fishes11040228

Authors: Jinpeng Zhang Yayu Wang Yunxiao Yang Hong Lin Yuhong Yang Dayan Hu

Rice–crab coculture, as China’s third-largest integrated farming model, is pivotal for sustainable Chinese mitten crab aquaculture. This study conducted untargeted metabolomics and 16S rRNA gene sequencing on gut contents of crabs from rice fields and ponds, integrating metabolic and microbial profiles. We aimed to reveal the chemical traits of rice-field Chinese mitten crab linked to gut microbiota, providing scientific guidance for optimizing culture practices and developing microbial additives. Both groups were dominated by the phyla Firmicutes, Proteobacteria, and Bacteroidota, but the phylum Bdellovibrionota was not detected in group R. A total of 1271 distinct amplicon sequence variants (ASVs) were identified, which were annotated to 649 genera. At the ASV level, the Chao1 index for the R group (197.12 ± 17.88) was notably lower compared to the P group (288.75 ± 30.59) (p < 0.01). In contrast, the Shannon index for the R group (3.90 ± 0.06) was significantly greater than that of the P group (3.70 ± 0.06) (p < 0.01). The PCA plot demonstrated a distinct discrimination between the groups. The P group had more microbial species but was dominated by Candidatus_Bacilloplasma, resulting in uneven distribution. In contrast, the R group had fewer species but a more balanced distribution. Among 3531 metabolites identified in both groups, 865 differed significantly. Compared to P, 736 metabolites were significantly upregulated and 129 were significantly downregulated in R. Key metabolic pathways included amino acid, carbohydrate, cofactor and vitamin metabolism, signaling, and xenobiotics biodegradation. Group R had higher levels of L-leucine, L-phenylalanine, L-tyrosine, 2-amino-1-phenylethanol, choline, and pyrophaeophorbide a, which correlated with genera like Candidatus_Hepatoplasma and Aeromonas (p < 0.05), suggesting better nutritional value, flavor, and metabolic health in rice-field crabs.

Fishes doi: 10.3390/fishes11040227

Authors: Thaís Brito Freire Flávia Lucena Zacchi João Paulo Ramos Ferreira Carlos Henrique Araujo de Miranda Gomes Claudio Manoel Rodrigues de Melo

Understanding the feeding physiological mechanisms of determined oyster species is fundamental for adaptation and growth stabilization, aiming for gains in aquaculture production. To assess its potential for Integrated Multi-Trophic Aquaculture (IMTA) with shrimp, we analyzed the feeding physiology of the mangrove oyster Crassostrea gasar. In this study, we determined the feeding physiology of the mangrove oyster Crassostrea gasar, a commercially important species in tropical Brazil, under two diets, live microalgae (ISO—Isochrysis galbana) and biofloc (BFT), which were tested at four concentrations (10, 20, 30, and 40 mg L−1), to establish whether this species can effectively utilize BFT as a food source. Results indicated that ISO diet promoted superior filtration, characterized by a higher proportion of feces (F), suggesting a reduced need for intensive particle selection. Both clearance (CR) and filtration (FR) rates peaked at 30 mg L−1 before declining, suggesting a physiological threshold for this diet. In contrast, the BFT diet elicited higher CR and FR values but triggered excessive pseudofeces (PF) production and low net organic selection efficiency (NOSE). This suggests high particle rejection and limited nutritional assimilation. In conclusion, while C. gasar can process BFT, it is metabolically disadvantageous as a sole food source. For an optimal performance, I. galbana concentrations should be maintained at or below 30 mg L−1.

Fishes doi: 10.3390/fishes11040226

Authors: Chun Mae Dong Mi-Nan Lee Hee Jeong Park Hyo Sun Jung Eun Soo Noh In Joon Hwang Jung-Ha Kang Eun-Mi Kim

Reliable identification of seafood species is critical for fisheries management and product authentication, especially when morphological characteristics are lost during processing. In this study, a multiplex PCR system was developed to distinguish seven cuttlefish species (six Sepia spp. and Sepiella inermis) commercially distributed in the Korean seafood market. Species identity was first confirmed by amplifying a mitochondrial cytochrome c oxidase subunit I (COI) fragment (~658 bp) using universal primers (LCO1490/HCO2198), showing 99–100% sequence similarity to corresponding GenBank reference sequences. Analysis of genetic variation based on a 530 bp aligned region demonstrated complete interspecific differentiation without shared haplotypes among species. The number of haplotypes per species ranged from 5 to 21, with haplotype diversity values between 0.667 and 1.000. An extended COI fragment (~1200 bp) was further analyzed to identify diagnostic interspecific variation for marker development. Seven diagnostic single-nucleotide polymorphism (SNP) sites were identified and used to design species-specific forward primers with diagnostic nucleotides positioned at the 3′ termini. Distinct amplicons (220–1099 bp) were generated and clearly resolved by agarose gel electrophoresis. Because simultaneous amplification of all seven primer pairs reduced amplification efficiency, the assay was divided into two multiplex sets. Under optimized conditions (56 °C), each species produced a single expected band without cross-amplification. This multiplex PCR system provides a rapid and sequencing-free approach for reliable species discrimination and can be effectively applied to fisheries monitoring and seafood authentication in commercial supply chains.

Fishes doi: 10.3390/fishes11040225

Authors: Fabián Guzmán-Rivas Juan Carlos Ortega Sergio Mora Ángel Urzúa

Understanding the reproductive physiology of marine fish is critical for sustainable fisheries management, particularly under environmental variability. This study evaluated seasonal changes in body parameters (condition factor, Kn, and gonadosomatic index, GSI, as proxies for body condition and reproductive status, respectively) and biochemical composition (P, proteins; G, glucose; L, lipids; fatty acids; and bioenergetic ratios L/P, LG, all as proxy of integrated biochemical condition) of female gonads in Strangomera bentincki, a key pelagic species in the Humboldt Current System (HCS) off south-central Chile. Moreover, environmental factors (sea surface temperature and chlorophyll-a) were also analyzed to explore their influence on the FA profile of gonads. Female body parameters showed significant seasonal variations, with high values of Kn and GSI in autumn and spring, respectively. The biochemical composition also revealed significant seasonal variation in protein and glucose content, with the highest protein levels in winter and elevated glucose in autumn. While total lipid and energy content remained relatively stable across seasons, the L/P and L/G ratios presented seasonal variations. Similarly, the fatty acid composition showed pronounced seasonal differences, particularly with increased polyunsaturated fatty acids (e.g., DHA) in winter. The SST was the environmental factor with the greatest influence on the seasonal variations in the gonadal FA profile. Altogether, these findings suggest a partial capital breeding strategy in S. bentincki, where reproductive investment depends on both accumulated reserves and environmental conditions during reproduction. This study underscores the importance of incorporating reproductive biochemical indicators into ecosystem-based fisheries management models to improve assessments of stock health and reproductive potential.

Fishes doi: 10.3390/fishes11040224

Authors: Shuo Feng Hua Xue Xirong Lin Ana Wu Wenqiao Tang

Ongoing urbanization continuously reshapes water quality, habitat structure, and biological communities in river ecosystems; however, its impacts on host-associated microbial communities remain poorly documented. The fish gut microbiota, a critical interface between the aquatic environment and host physiology, is widely recognized as an integrative indicator of both environmental change and host ecological traits. This study established a continuous urbanization gradient along Shanghai’s Suzhou River, spanning from suburban areas through the outer and inner ring roads to the city center. Five common wild fish species (Coilia nasus, Hemiculter bleekeri, Culter alburnus, Acheilognathus macropterus, and Pseudorasbora parva) were collected, and their gut microbiota were characterized via high-throughput 16S rRNA gene sequencing. Significant variation in OTU richness, alpha diversity, and community structure was observed across urbanization gradients and among fish species. Principal coordinate analysis revealed that samples from suburban areas were structurally distinct from those collected in other zones, whereas inner-ring and urban-core areas exhibited substantial compositional overlap. Taxonomic analysis revealed that Firmicutes and Pseudomonadota dominated all samples; however, their relative abundances and genus-level composition varied considerably among fish species and across the urbanization gradient. PICRUSt-based functional prediction indicated that metabolic pathways predominated, particularly those involved in global and overview maps, carbohydrate metabolism, amino acid metabolism, energy metabolism, and metabolism of cofactors and vitamins. Collectively, these findings demonstrate that fish gut microbial communities exhibit spatial structuring along the urbanization gradient, with species-specific responses linked to ecological traits. This study provides valuable data on host-associated microbial communities in urban rivers and offers a reference for incorporating microbial indicators into urban water ecological assessments.

Fishes doi: 10.3390/fishes11040223

Authors: Qiushi Yang Zhimin Zhang Tingting Xu Wenhan Li Huacheng Li Rong Tang Yale Deng Liqin Yu Xi Zhang Li Li Dapeng Li

Diet form is increasingly recognized as a welfare-relevant factor in intensive aquaculture, yet the effects of feed cooking on fish behavioral and physiological welfare remain poorly characterized. Juvenile southern catfish (Silurus meridionalis; 6.18 ± 0.52 g) were reared for 6 weeks in an indoor recirculating aquaculture system and fed either raw grass carp (Ctenopharyngodon idella) muscle (fish fed raw muscle, FR) or cooked grass carp muscle (fish fed cooked muscle, FC; 15 min ramp to ~100 °C followed by 2–3 min at ~100 °C). Locomotor activity and anxiety-like behavior were assessed using the open-field test and an annular light–dark preference assay, respectively. Flow-through respirometry further revealed a significantly lower standard metabolic rate (SMR) in FC fish than in FR fish, decreasing from 10.30 to 6.83, which represents a 33.7% reduction. Endocrine and biochemical analyses showed that cooking significantly decreased serum total triiodothyronine (T3) by 23.8%, whereas routine serum biochemical indices remained unchanged. In brain tissue, dopamine (DA) was significantly reduced by 7.2% in the FC group, and RT-qPCR analysis of dopamine-related genes further showed a significant downregulation of the rate-limiting synthesis gene th. These results indicate that cooking primarily downshifts the activity-energy axis in southern catfish and is accompanied by coordinated thyroid and dopaminergic changes. To our knowledge, this is the first integrated study to evaluate the behavioral, metabolic, and neuroendocrine effects of cooked feed in S. meridionalis, providing a short-term phenotypic baseline for assessing welfare-relevant feeding scenarios in aquaculture.

Fishes doi: 10.3390/fishes11040221

Authors: Shiliang Dong Maninder Meenu Huamao Wei Yuhang He Zhoudi Miao Jinxing Xiao Ying Liu

The large yellow croaker (Larimichthys crocea) is a high-value marine fish, but stress during live transport often leads to physiological disturbance and deterioration of muscle quality. This study investigated the effects of pre-transport temporary rearing at three temperatures (8, 10, and 12 °C) over 48 h on stress response, energy allocation, and muscle quality in this fish species. Temporary rearing at 8 °C induced stronger cold stress, characterised by elevated cortisol, marked lipid mobilisation, late lactate rebound, and greater loss of polyunsaturated fatty acids, indicating enhanced stress–catabolism coupling and higher risk of quality deterioration. In contrast, 12 °C did not sufficiently suppress metabolic turnover, resulting in continuous glycogen depletion, rapid ATP degradation, and accelerated accumulation of bitter-tasting nucleotide metabolites such as hypoxanthine. Among the tested temperatures, 10 °C showed the most coordinated response, with relatively stable endocrine status, moderate substrate utilisation, lower accumulation of undesirable degradation products, and better preservation of texture, water-holding capacity, and flavour-related precursors. These findings suggest that 10 °C is a promising pre-transport temporary rearing temperature for large yellow croakers under the present 48 h experimental conditions. The advantage of this temperature appears to lie in achieving a more favourable balance between metabolic suppression and physiological homeostasis, thereby providing a scientific basis for improving pre-transport rearing management and supporting safer, more stable live transport. Future studies incorporating behavioural and molecular indicators are needed to further clarify the regulatory effects of 10 °C during pre-transport rearing.

Fishes doi: 10.3390/fishes11040222

Authors: Shenwan Ding Wenqiao Cai Yaohai Xu Cai Jin Xiangrui Ma Liang Rao Yang Gao Haidong Li Zhangjie Chu

This study investigated the effects of dietary Bacillus cereus, administered alone or in combination with biofloc technology, on the growth performance, immune response, disease resistance, and intestinal microbiota of Litopenaeus vannamei. Shrimp fed diets supplemented with B. cereus, either directly or via biofloc systems, exhibited significantly increased final body weight and specific growth rate, together with a reduced feed conversion ratio compared with the control group. The expression levels of key hepatopancreatic immune-related genes, including lysozyme, prophenoloxidase, superoxide dismutase, Toll, immune deficiency, and Relish, were significantly upregulated in probiotic-associated treatments. Following challenge with Vibrio parahaemolyticus, cumulative mortality was markedly lower in all treatments involving B. cereus or biofloc compared with the control. Although alpha diversity indices were not significantly affected, beta diversity analysis demonstrated that supplementation frequency and delivery mode altered intestinal microbial community structure. The phyla Bacteroidota, Firmicutes, and Proteobacteria predominated across treatments, while members of Marinilabiliaceae and Shewanellaceae were enriched under probiotic-associated conditions, suggesting enhanced nutrient transformation potential. Co-occurrence network analysis further revealed increased microbial network complexity and positive interactions in probiotic and biofloc treatments, indicating improved community stability. These findings demonstrate that the synergistic application of B. cereus and biofloc technology enhances growth performance, immune capacity, and intestinal microbial resilience in intensive shrimp culture, and that supplementation strategy plays a critical role in optimizing probiotic efficacy.

Fishes doi: 10.3390/fishes11040220

Authors: Tao Teng Dehong Zhang Jianhua Ming Hualiang Liang Li Cai Tingting Li Xiufang Ren Lu Zhang Haifeng Mi

This study aimed to investigate the effects of dietary lipid levels on growth performance and transport stress resistance in large-sized channel catfish (Ictalurus punctatus). Four experimental diets were formulated with fat levels of 7.5% (control), 10.0%, 12.5%, and 15.0%, using soybean oil as the lipid source. Each diet was assigned to four replicate groups in a 110-day feeding trial, with fish averaging 600.61 ± 1.33 g at the start. Results showed that increasing dietary fat enhanced weight gain rate (WGR) and specific growth rate (SGR), with the 15.0% fat group achieving the best growth performance and the lowest feed conversion ratio (FCR), significantly lower than the control (p < 0.05). However, fish fed diets containing 12.5% and 15.0% fat exhibited disorganized hepatocyte arrangement, unclear cell boundaries, and hepatic vacuolization. Serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities increased initially and then declined with rising fat levels, with the highest values observed at 12.5% fat, significantly exceeding those in the control group (p < 0.05). Furthermore, after simulated transport, the incidence of skin congestion and hemorrhage increased with dietary fat level. Collectively, while higher fat levels improved growth, excessive fat (≥12.5%) compromised liver health and stress resilience. Therefore, a dietary fat level of 10.0% is recommended to balance optimal growth, hepatic integrity, and transport tolerance in I. punctatus.

Fishes doi: 10.3390/fishes11040219

Authors: Andrea Novaković Jovana Jovanović Marić Stoimir Kolarević Lucija Markulin Teja Petra Muha Irena Todorović Jelena Stanković Ristić Tamara Mitić Stefan Andjus Jelena Čanak Atlagić Ana Marić Margareta Kračun-Kolarević

Understanding salmonid spawning dynamics is critical for conserving cold-water river ecosystems amid increasing human and climate pressures. This study developed and validated a species-specific eDNA (Salmo cf. trutta and Thymallus thymallus) and evaluated its performance for seasonal spawning activity monitoring using droplet digital PCR (ddPCR). Species-specific primers and probes targeting mitochondrial nd5 (S. trutta) and cytb (T. thymallus) genes were designed and optimized as a duplex assay. Performance assessments included in vitro validation, cross-amplification testing, and determining the LOB, LOD, and LOQ. Field validation over a year at two spawning sites in the Gradac River, Serbia, involved seasonal eDNA sampling, filtration, extraction, and ddPCR analysis. Fish community composition was also assessed with electrofishing and metabarcoding. The assay showed high specificity and sensitivity, with LODs of 0.14 cp/µL and LOQs of 0.99 and 1.25 cpµL for S. trutta and T. thymallus. S. trutta eDNA peaked in late autumn during spawning, while T. thymallus remained at or below detection limits, reflecting its lower abundance and different spawning season. Filter type affected filtration efficiency but not eDNA yield. These findings confirm ddPCR-based eDNA as a powerful, non-invasive tool for monitoring salmonid spawning and seasonal changes, supporting adaptive fisheries management and conservation amid environmental changes.

Fishes doi: 10.3390/fishes11040218

Authors: Aristeidis Tsopelakos Christina Dalla Helen Miliou

Understanding how different pre-slaughter and slaughter procedures modulate physiological and neurochemical pathways in European sea bass (Dicentrarchus labrax) remains essential for welfare-oriented aquaculture. This study comparatively evaluated six procedures: clove oil and 2-phenoxyethanol anaesthesia, percussive stunning, asphyxiation in ice slurry or on solid ice, and clove oil anaesthesia followed by ice slurry, using plasma glucose and whole-brain monoaminergic indices as integrative physiological response indicators. Ninety-six fish were analysed. Ice-based asphyxiation and 2-phenoxyethanol exposure were associated with the highest plasma glucose concentrations, whereas clove oil and percussive stunning showed comparatively lower values. Dopaminergic and serotonergic turnover ratios (DOPAC/DA; 5-HIAA/5-HT) increased sharply under ice and 2-phenoxyethanol treatments, indicating increased monoaminergic activity under these procedures. Multivariate analyses (MANOVA, PCA) distinguished anaesthetic-based treatments from ice-based methods according to their combined neurochemical profiles. Although correlations between glucose and monoaminergic indices were modest, they were statistically significant and consistent with coordinated metabolic–neurochemical adjustments. Overall, DOPAC/DA and 5-HIAA/5-HT ratios emerged as sensitive and mechanistic biomarkers capable of differentiating slaughter procedures according to their relative physiological impact. These findings support the integration of metabolic and neurochemical indicators in welfare assessment and may contribute to evidence-based refinement of humane slaughter protocols in Mediterranean aquaculture systems.

Fishes doi: 10.3390/fishes11040217

Authors: Rafel Rocaspana Carles Alcaraz Enric Aparicio

Brown trout (Salmo trutta) populations at the southern edge of the species’ distribution are increasingly exposed to interacting climatic, biotic, genetic, and anthropogenic pressures. This study provides an integrative assessment of the drivers of variation in brown trout density, biomass, and size structure across six Mediterranean river basins in Catalonia (NE Iberian Peninsula), based on long-term standardized electrofishing surveys (2016–2025; 88 sites). Generalized linear mixed models revealed that mean summer temperature, genetic introgression from hatchery-derived Atlantic lineages, and the density of introduced fish species were the most consistent negative predictors of total density, biomass, and juvenile abundance (<120 mm FL). Hydrological and nutrient variables showed comparatively weak or non-significant effects relative to thermal and biotic predictors. Fishing regulations significantly influenced the biomass and density of larger trout (>220 mm FL), with lower values in harvest-allowed sections, whereas total density was less responsive to regulation. These findings indicate that Mediterranean brown trout populations are primarily constrained by thermal conditions, genetic integrity, and biological invasions, with implications for conservation and fishery management under ongoing climate warming.

Fishes doi: 10.3390/fishes11040216

Authors: Haijing Liu Miaomiao Wang Junhao Huang Jiang Li Chunyan Zheng Huan Zhang Jing Xu Qihui Yang Gangfu Chen Huatao Li

This research was conducted to evaluate the impacts of pomegranate (Punica granatum L) peel extract (PPE) on the mold growth and moisture content in pellet feeds, as well as the biochemical indicators in tissues and organs of fish. Firstly, six types of pellet feeds were formulated by adding 0% or 0.5% of pomegranate peel powder (PP), petroleum ether extract (PEE), ethyl acetate extract (EAE), ethanol extract (EE), or aqueous extract (AQE) of PP. Moisture content was determined by air-drying 10 g of wet pellet feed from each treatment at 60 °C for 48 h in uniform-sized Petri dishes. Mold growth was evaluated by homogenizing 15 g of 12-week stored pellet feed with 15 mL of purified water, incubating at 25 °C for 4 days, and recording mold growth. The results indicated that PP, PEE, EE, and AQE reduced the mold growth in pellet feeds (p < 0.05). PP, EAE, EE, and AQE increased the moisture content in pellet feeds. Among all additives, EE has the strongest effects on the mold growth and moisture content in feeds (p < 0.05). According to regression analysis of mold and moisture levels, the optimal EE supplementation levels in pellet feeds were evaluated to be 1.284% and 1.485%, respectively. Then, 420 carp (Cyprinus carpio var. Jian, mean initial weight 12.01 ± 0.53 g) were fed diets formulated with EE at graded inclusion levels (0, 0.3, 0.6, 0.9, 1.2, 1.5, and 1.8%) over a 15-day period. The findings indicated that dietary EE improved the digestive and absorptive function in carp (p < 0.05), and this improvement was closely correlated with the upregulated activities of digestive and absorptive enzymes and the strengthened antioxidant capability in carp’s digestive tissues. Regression analysis of feed intake rate indicated that the optimal EE level suitable for carp is 0.906%. Furthermore, dietary EE enhanced the respiratory capacity by improving functional metabolic enzyme activity and antioxidant defense in the respiration-related tissues and organs of fish (p < 0.05). In summary, supplement EE increases the moisture content, inhibits the mold growth in pellet feeds, and improves the respiratory, digestive, and absorptive functions in fish, providing a valuable insight for PEE use as a naturally functional raw material in fish feeds.

Fishes doi: 10.3390/fishes11040215

Authors: Gen Li Jin Wang Anji Lian Lijun Gou Guoliang Pang Taiping Yuan Yu Hu Xiaohua Huang

Net cleaning robots have been playing an increasingly important role in offshore aquaculture due to their efficiency and labor-saving capabilities. However, in practice, these robots are still entirely teleoperated and require constant, skilled human operation. The mesh intersection points, which serve as a structural feature of the nets, provide valuable visual cues for robot self-localization and net damage identification. Therefore, the detection and tracking of these points are crucial for developing autonomous net cleaning robots. To achieve intersection point detection, we propose NPUNet-lite, a lightweight model based on U-Net. This model significantly minimizes computational resources and model size while preserving high detection accuracy. For reliable point tracking, we develop the NlPTrack algorithm, which incorporates an iterative closest point-based association strategy to meet spatial constraints between points within a frame, and a cascaded association strategy to satisfy homographic and epipolar constraints across adjacent frames. We build a dataset from videos collected during a robotic cleaning task to train and evaluate our methods. The experimental results indicate that our segmentation network achieves comparable accuracy to advanced networks, yet with a substantial reduction in computational cost. Meanwhile, the tracking method successfully tracks the majority of intersection points across scenarios where the robot moves in different directions.

Fishes doi: 10.3390/fishes11040214

Authors: Ki-Taek Cho Dong-Hoon Lee Beom-Hee Lee Bo-Seong Kim

This study reports the first isolation of Elizabethkingia miricola from cultured river puffer (Takifugu obscurus) in South Korea under low-salinity aquaculture conditions. A total of 5000 juvenile T. obscurus were reared for 20 months in a recirculating aquaculture system with salinity maintained at 3–5 ppt. During the rearing period, fish exhibited a cumulative mortality rate of 58.17%, presenting clinical signs such as lethargy, fin rot, hepatic hemorrhage, and white nodules in the spleen and kidney. Biochemical and molecular analyses identified E. miricola in the internal organs of diseased fish. All isolates exhibited multidrug resistance and showed 98.8–99.8% 16S rRNA gene sequence similarity to E. miricola, forming a distinct phylogenetic cluster. Additionally, several virulence-associated genes (fabG, fabV, wecB, ureB, aceA, acyl) were detected in the isolates. Histopathological examination revealed granulomatous lesions in multiple organs, including the gill, heart, kidney, and spleen. This study represents the first report of E. miricola isolated from cultured river puffer in South Korea and suggests its potential association with disease in this species, as well as its possible zoonotic relevance. These findings highlight the importance of disease monitoring and pathogen surveillance in low-salinity aquaculture systems.

Fishes doi: 10.3390/fishes11040213

Authors: Jesús Dámaso Bustamante-González Gerardo Figueroa-Lucero María Cecilia Hernández-Rubio Judith Sarai Baca-Alejo Edith Arenas-Ríos Araceli Cortés-García Leticia González-Núñez Mariela Adriana Ydiaquez-Miranda Alejandro Ávalos-Rodríguez

Chirostoma humboldtianum is an endemic atherinopsid from Mexico that has been of high socio-cultural and economic importance since pre-Hispanic times. It was the first ictic species from Mexico described for science, and it is considered the basal species that gave rise to a nominal group known as white fish or silversides. The aim of this research was to analyze semen quality in relation to breeding fish size and its effect on sperm cryopreservation during an annual cycle. Sexually mature males were collected from January to December 2023, in San Felix dam, Tiacaque, Mexico State, Mexico. The water temperature was measured, and the photoperiod was obtained from the Instituto Nacional de Geografía y Estadística (INEGI). Males were classified into two groups of total length (TL) after analyzing the variation in TL through a size histogram: (G1) 9–13 cm and (G2) longer than 13 cm. Semen volume (µL), sperm concentration (cells µL−1), and motility percentage (%) were determined in all individuals of each group. Likewise, eight straws were cryopreserved per month per group, each one with 10 µL of semen from a mixture of three randomly selected individuals and cryopreserved at −196 °C for 72 h. The post-thawing motility percentage was subsequently verified. Males produce semen continuously all year round, with two periods of higher volume, March and June–August, defining two reproductive periods. The beginning of the first one coincides with the increase in water temperature, from 13 ± 2 to 18 °C. Males with a length more than 13 cm had a higher semen production compared to smaller males (17.33 ± 7.34 and 12.52 ± 4.41 µL, respectively, p < 0.05). The largest semen volumes were registered in March and from June to August in both groups. However, G2 males presented with a larger semen volume. Both groups had a marked decrease in a similar manner in April–May and September to January (p < 0.05). Sperm concentration was similar throughout the year in both groups (p > 0.05) (G1 = 1.35 ± 0.36 × 106 µL−1) (G2 = 1.31 ± 0.35 × 106 µL−1). In addition, fresh sperm motility was high in both groups (G1 = 96 ± 3%, G2 = 97 ± 4%) (p > 0.05). The highest sperm concentrations were observed in March to July, through to October for both groups (p > 0.05), while post-thaw sperm motility decreased by about 50% (G1 = 45 ± 4%) (G2 = 46 ± 6%) during the annual cycle (p > 0.05). The largest post-thaw motility was observed in March and from July to September in G1 and in March and from June to October in G2. Analysis of semen quality throughout the annual cycle reveals aspects of the reproductive biology of C. humboldtianum, including two reproductive peaks and continuous semen production.

Fishes doi: 10.3390/fishes11040212

Authors: Dai Zhang Huang Liu Andong Liu Chongwu Guan Chenglin Zhang Yujie Chen Yiqi Wu Yue Zhang

In the fish grading process, traditional mechanical sorting devices tend to cause fish stacking, collisions, and increased stress responses, seriously affecting fish health and commercial value. This paper designs a power-free fish pre-sorting device based on a spiral chute structure, achieving automatic and gentle separation and output driven by the fish’s own weight and water flow; it constructs a multi-stage dynamic model of fish in the spiral chute to analyze the forces and motion patterns; and it introduces an innovative DEM-SPH coupled numerical simulation technology to accurately simulate the complex interactions between fish and water, thereby revealing the self-sorting mechanism of fish inside the device. By setting different conditions such as fish length and water layer thickness, the sorting effect and stability of the device are systematically verified. The results show that this spiral power-free sorting device can effectively achieve automatic spacing separation of fish, reducing collisions and stress responses; fish of 130 mm length have better sorting stability under a water layer thickness of 3–5 cm, and the minimum initial release spacing for effective operation of the device is determined to be 0.11 m.

Fishes doi: 10.3390/fishes11040208

Authors: Joshua L. Superio Hasmin F. Villanueva Frenz Charish B. Hechanova Kenaz Barnie P. Cejar Fiona L. Pedroso Casiano H. Choresca

The African catfish (Clarias gariepinus) is an important aquaculture species in the Philippines, but it exhibits reproductive dysfunctions in captivity due to the absence of natural spawning cues and culture-induced stress. In hatcheries, sperm collection often requires sacrificing male breeders, limiting breeding program applications, and threatening genetic diversity. This study evaluated and optimized hormonal induction protocols to enhance spermiation and fertilization success in male C. gariepinus. Two experimental trials were conducted under controlled hatchery conditions. In Trial 1, human chorionic gonadotropin combined with a dopamine antagonist (hCG + DA; 5000 IU·kg−1 BW + 5 mg·kg−1 BW) and Ovaprim (1.0 mL·kg−1 BW) significantly increased circulating testosterone and estradiol levels, spermiation index, and fertilization outcomes (embryo viability, hatching, and larval survival). In Trial 2, medium to low doses of hCG + DA (3000–5000 IU·kg−1 BW + 5 mg·kg−1 BW) and Ovaprim (0.75–1.0 mL·kg−1 BW) yielded the best performance in terms of hormone levels, spermiation index, and fertilizing capabilities. The presence of a dopamine antagonist (DA) likely contributed to the efficacy of the treatments, since dopamine suppresses the secretion of gonadotropin-releasing hormone (dopaminergic inhibition), and DA counteracts this effect, increasing LH and FSH levels necessary for gametogenesis. Taken together, these results highlight the potential of optimized hormonal protocols to mitigate reproductive dysfunctions in male C. gariepinus in aquaculture settings. Further studies should refine dose combinations, assess the long-term health of broodstock, and evaluate cost-effectiveness to support sustainable broodstock management and genetic conservation.

Fishes doi: 10.3390/fishes11040211

Authors: Marianna Oteri Ambra Rita Di Rosa Vittorio Lo Presti Giovanni Toscano Filippo Giarratana Biagina Chiofalo

The search for sustainable alternatives to fishmeal (FM) in aquafeeds represents a major challenge for modern aquaculture. This study evaluated the effects of replacing 35% of FM with defatted Hermetia illucens larvae meal (HIM35) in diets of gilthead seabream (Sparus aurata) reared under full-scale commercial offshore farming conditions. Fillet nutritional quality, fatty acid and amino acid profiles, mineral composition, and microbiological stability during refrigerated storage were assessed. Dietary HIM35 significantly modified the fatty acid profile, increasing saturated fatty acids, particularly lauric and myristic acids, and n-6 polyunsaturated fatty acids. Despite reductions in eicosapentaenoic and docosahexaenoic acids (EPA and DHA), total PUFA and lipid health indices remained within recommended ranges and EPA + DHA levels were above 8%, supporting both fillet nutritional value and fish physiological requirements. Enzymatic indices based on product-to-precursor fatty acid ratios suggested reduced Δ5 + Δ6-desaturase activity. The amino acid profile showed increases in selected essential and non-essential amino acids, while overall protein quality was preserved. HIM35 fillets showed lower sodium and higher zinc contents, whereas increased aluminum levels warrant further investigation. Microbiological analyses confirmed the absence of foodborne pathogens and no effects on spoilage dynamics. Overall, HIM35 represents a safe and effective partial replacement for FM supporting sustainable aquafeed strategies.

Fishes doi: 10.3390/fishes11040210

Authors: Lambros E. Kokokiris George Minos Cosmas Nathanailides Maria Papadaki Constantinos C. Mylonas

The aim of this study was to evaluate the effects of a gonadotropin-releasing hormone analogue (GnRHa), administered through injections or with sustained-release implants, on spermiation and sperm quality in thicklip grey mullet, Chelon labrosus. Male broodstock transferred from extensive lagoons were randomly allocated to three treatment groups: (a) weekly saline injections (Saline-INJ), (b) weekly GnRHa injections (10 μg kg−1 bw; GnRHa-INJ), and (c) a single GnRHa EVAc implant (50 μg kg−1 bw; GnRHa-IMP). Males were maintained with females under the same treatment protocols and allowed to spawn. Sperm condition, density, motility, duration of motility, and androgen levels were evaluated weekly at five sampling points (Days 0, 7, 14, 21, and 28). All males exhibited complete spermiation during the first two weeks (Days 0 and 7), followed by a gradual decline throughout the rest of the study (Days 14 and 21). This pattern of decline was not as evident in the groups treated with GnRHa, especially in the GnRHa-INJ group. Sperm density, motility, and motility duration varied strongly over time; however, no significant differences were observed among treatments. GnRHa treatment prolonged the spermiation period and delayed its seasonal decline without significantly altering sperm quality. These results may enable more frequent sperm collection and greater sperm availability, as inferred from the spermiation condition (SCI) and qualitative observations.

Fishes doi: 10.3390/fishes11040209

Authors: Xirui Xu Fei Wang Weimin Quan Ruiliang Fan Wei Fan Sanling Yuan

The spatial distribution of oyster reefs is an important indicator for assessing environmental changes in nearshore fishery habitats. However, due to tidal fluctuations, images of oyster reef distribution acquired under low-light conditions such as early morning or evening often exhibit common issues such as bright spots and shadows. Thermal infrared (TIR) images, which are unaffected by external lighting conditions, can effectively address this problem. Aerial imaging of Liya Mountain, Haimen, Jiangsu Province, China, was conducted in this study. Based on unmanned aerial vehicles (UAVs) imagery acquired in 2025 using multispectral and TIR sensors, the total oyster reef area was estimated to be 6.61 ha. When compared with the oyster reef distribution derived from visible light aerial imagery collected in 2023 under favorable environmental conditions, this represents a decrease of 0.36 ha (5.4%), with the largest individual reef measuring 3388.17 m2. To demonstrate the improvement in extraction accuracy achieved by integrating TIR data with multispectral imagery, the research team compared the extraction accuracy for oyster reefs of different sizes: a 1.91% improvement was observed for small reefs, a 9.02% improvement for middle reefs, and an 18.98% improvement for large reefs. Experimentally, the emissivity of oyster reefs was determined to be 0.982 ± 0.002 using an isothermal method in the laboratory. The emissivity derived from in situ measurements showed similar values, supporting the reliability of the laboratory result and providing a crucial parameter for the inversion of reef surface temperature. Experimental results demonstrate that the TIR band can effectively enhance the spatial accuracy of oyster reef measurements under low-light conditions.

Fishes doi: 10.3390/fishes11040207

Authors: Mikhail Kutuzov Maria Belova Hicham Zaroual Igor Nikitin Olga Novichenko Dmitry Zhukov Daria Vilkova

Rainbow trout (Oncorhynchus mykiss) farming represents a significant opportunity for developing sustainable regional aquaculture and food systems. This study assesses its potential using the Vologda Region in Northwest Russia as a case study. The methodology involved analyzing the compatibility of the species’ ecological requirements with local hydrochemical conditions and evaluating production dynamics from 2016 to 2024 through trend analysis. The results confirm that key water bodies in the region provide suitable conditions for industrial-scale cage farming. Production exhibited exponential growth, increasing from 10 to 994 tonnes over the eight-year period, transitioning from a rapid expansion phase (2016–2020) to a phase of stable, sustainable growth (2021–2024) with annual increases of 100–150 tonnes. A SWOT analysis identified major strengths, including abundant water resources and government support, alongside critical challenges such as technological lag, dependence on imported inputs, and skilled labor shortages. The findings underscore the substantial potential of trout aquaculture to serve as a pillar of a localized food system in the region. Realizing this potential over the long term will require targeted investments in modern technology, value-added processing, and workforce development to mitigate existing constraints.

Fishes doi: 10.3390/fishes11040206

Authors: Tihomir Roussinov Stefanov Pencho Georgiev Pandakov Dimitar Zhelyazkov Dimitrov Violeta Ivanova Evtimova Nikolay Minchev Todorov

The Varna–Beloslav Lake Complex has been subjected to intense anthropogenic pressure over the past century. The excavation of a navigation channel connecting the two lakes with the Black Sea, together with the intensive industrial development in the surrounding area, has led to irreversible alterations in the species composition of the ichthyofauna. This study aimed to document and analyze these changes based on data collected during a four-year survey using a range of ichthyological methods. A total of 28 fish species were recorded, representing approximately one-third of the species historically reported for the complex. Hydromorphological degradation, combined with salinization, heavy ship traffic and pollution, has been identified as the main cause of the observed decline in fish diversity within the system.

Fishes doi: 10.3390/fishes11040205

Authors: Jiang Zhou Baosuo Liu Huayang Guo Nan Zhang Lin Xian Qin Zhang Kecheng Zhu Dianchang Zhang

The yellowfin seabream (Acanthopagrus latus) is an important aquaculture species, yet endocrine gene regulation during practical fasting and feeding schedules remains poorly understood. Here, we identified and characterized two duplicated proglucagon genes (Gcga and Gcgb) and examined tissue distribution of expression and transcriptional responses to feeding-related challenges. Sequence and phylogenetic analyses confirmed that Gcga and Gcgb cluster with teleost proglucagon paralogs and contain conserved peptide domains. Both genes were broadly expressed, with the strongest relative qRT-PCR signal detected in brain and fin, while other tissues (including intestine, gill, stomach, and liver) showed comparatively low but detectable expression. Because the liver is a central metabolic organ and displayed reproducible feeding-dependent regulation, we further quantified hepatic transcription under two paradigms. In a short-term starvation–refeeding trial, hepatic Gcga was significantly suppressed during fasting and rebounded after refeeding, whereas Gcgb showed a distinct, weaker response. In an acute peri-feeding assay, hepatic Gcga and Gcgb displayed rapid but differential regulation around meal time, and Gcgb expression differed between feeding and non-feeding groups. Together, these results support transcriptional divergence between the two proglucagon paralogs in nutritional regulation within a liver-focused metabolic-response model. Our findings provide baseline molecular information for A. latus and offer endocrine insights relevant to evaluating feeding strategies in aquaculture.

Fishes doi: 10.3390/fishes11040204

Authors: Xiaorui Fan Yuqiang Wei Jianguo Zhao Yajun Wang Jianhua Zhao Qiyou Xu

This study investigated the effects of dietary lysophospholipids on growth performance, hepatic lipid metabolism, intestinal health, and dietary lipid levels of largemouth bass. The 56-day experiment included five groups: CON (0% lysophospholipids), LL50 (0.05% lysophospholipids), LP50 (0.05% lysophospholipids—0.5% oil), LP100 (0.1% lysophospholipids—1.0% oil), and LP200 (0.1% lysophospholipids—2.0% oil), with 3 replicates (30 fish/replicate) per group. The results showed that compared with the CON group, dietary supplementation of 0.05% lysophospholipid had no significant effect on the growth performance of largemouth bass, but increased the crude protein content and decreased the crude lipid content in the whole body. An amount of 0.05% lysophospholipid improved hepatic lipid utilization efficiency. Specifically, this supplementation level promoted serum lipid transport (increased serum HDL-C content and decreased triglyceride and LDL-C contents), and enhanced hepatic lipid metabolism by regulating the expression of lipid metabolism-related genes (fas, hsl, and acc) and the levels of lipid metabolites (phosphatidylcholine and fatty acids), thereby reducing hepatic triglyceride content. In addition, 0.05% lysophospholipid improved intestinal health by increasing lipase activity and intestinal villus height, up-regulating the expression of the anti-inflammatory gene (tgf-β1) and tight junction protein genes (claudin-1, claudin-4, and zo-1), and down-regulating the expression of the pro-inflammatory gene (tnf-α). In terms of dietary lipid reduction, supplementation with 0.1% lysophospholipid allowed a 1% reduction in dietary lipid level without affecting the growth performance of largemouth bass, whereas at the same level of lysophospholipid supplementation, a 2% reduction in dietary lipid level resulted in decreased growth performance of largemouth bass. These findings provide theoretical support for the practical application of lysophospholipids, and demonstrate that reducing dietary lipid inclusion by adding lysophospholipids helps to reduce feed costs and improve aquaculture economic benefits.

Fishes doi: 10.3390/fishes11040203

Authors: Guiqin Chen Zengguang Li Tongzheng Zhang

Drifting fish aggregating devices (DFADs) are central to tropical tuna purse-seine fisheries, yet their hydrodynamic performance under realistic seas has not been adequately addressed, particularly for emerging eco-friendly designs. A three-dimensional framework based on computational fluid dynamics is developed to assess the motion response and mooring loads of full-scale DFADs comprising raft buoys, biodegradable cotton rope, and iron sinkers, using four buoy layouts (Models A to D). Unsteady Reynolds-averaged Navier–Stokes (URANS) simulations are performed with a realizable k–ε closure, volume of fluid (VOF) free-surface capturing, the Euler overlay method, dynamic overset meshes, and catenary mooring coupling. Regular waves representative of operational conditions (T = 1.40 to 2.40 s, H = 0.10 to 0.40 m) are imposed via a VOF wave-forcing technique, and mesh/time-step sensitivity analyses demonstrate the accurate reproduction of the first-order wave elevation (error < 0.8%). Surge drift per cycle and heave response amplitude operators, with the relative mooring force, are evaluated as functions of the relative wavelength (λ/La) and wave steepness (H/λ). The results reveal that the buoy layout exerts first-order control on DFAD dynamics, whereas short, steep waves dominate motion and line loads. The intermediate end-point sinker mass achieves a favorable balance between motion suppression and mooring load control, whereas distributing a fixed total sinker mass along the rope reduces heave response and mooring force by improving the tension redistribution and overall stability. Across all sea states, Models A and D reduced motion envelopes and mooring forces, indicating their suitability as robust, low-impact configurations. The proposed framework and design recommendations provide quantitative guidance for optimizing eco-DFAD geometry and deployment strategies, supporting safer and more sustainable DFAD-based tuna fisheries.

Fishes doi: 10.3390/fishes11040202

Authors: Yingsha Qu Huichen Li Bo Zhang Hongwu Cui Jianlei Chen Yong Xu Zhengguo Cui Keming Qu Hao Li

Saline–alkaline water constitutes a vital strategic non-traditional fishery resource in China, characterized by high pH values, elevated carbonate alkalinity, and complex ionic compositions. These extreme environmental conditions impose significant stress on aquatic animals, mainly by inducing ionic toxicity and disrupting acid–base regulatory mechanisms. Such disruptions subsequently lead to osmotic imbalance, metabolic dysregulation, and immunosuppression, thus restricting the survival and growth of aquatic species in aquaculture systems. Consequently, the sustainable development of the saline–alkaline aquaculture is imperative for enhancing production efficiency and promoting the utilization of marginal land and water resources. This review comprehensively summarizes the current status of saline–alkaline aquaculture and highlights the stress-inducing impacts of salinity, alkalinity, and specific ionic ratios on teleost fishes and crustaceans. It further explores key adaptive mechanisms, including osmoregulatory and ionoregulatory strategies, bioenergetic trade-offs related to oxygen consumption and ammonia excretion, coordinated antioxidant and innate immune responses, as well as recent findings from multi-omics research. This review aims to offer a scientific foundation for the selection and breeding of saline–alkaline-tolerant strains, the precise regulation of aquaculture water environments, and the development of ecological aquaculture models in saline–alkaline regions, thereby facilitating the sustainable utilization of saline–alkaline land and water resources.

Fishes doi: 10.3390/fishes11040201

Authors: Marco Shizuo Owatari

Nutrition plays a vital role in the aquaculture industry, particularly in fish farming, as it significantly influences operational costs, zootechnical performance, animal health, product quality, and the sustainability of production systems [...]

Fishes doi: 10.3390/fishes11040200

Authors: Zhe Wang Minrui Lai Hongze Li Yudong Wang Rukui Zeng Jianzhang Lv Tao He Changhai Han Xiaogang Wang

Visual cues are critical for orientation and migration in riverine fishes, providing potential mechanisms for behavioral guidance. This study investigated how light spectrum and intensity interact to modulate phototactic responses in two schizothoracine fishes from the upper Yalong River. Results showed Schizopygopsis malacanthus preferred blue light and avoided red light, with preferences shifting with flow intensity; Schizothorax kozlovi favored green light and avoided light-red light, with minimal flow impact. We propose that engineers build fishway entrances or ideal habitat attractors that prioritize low-intensity blue light (10 lx) and medium-intensity green light (50 lx), supplemented by medium-intensity blue light (50 lx). This study provides scientific evidence and application value for restoring fish habitats, fish passages, and fisheries.

Fishes doi: 10.3390/fishes11040199

Authors: José Artur Marcelino Virgínia Fonseca Pedrosa Luis Alberto Romano Ronaldo Olivera Cavalli

Broodstock conditioning involves maintaining adult animals in optimal environmental conditions to ensure that the largest number of breeders reach maturity. We evaluated the gonadal development and the occurrence of spawns in the yellow clam (Amarilladesma mactroides) and estimated the duration of conditioning that results in the highest maturity rate. Clams were kept buried in a 10 cm sand bed within Ø = 15 cm containers. A concentrate of Isochrysis galbana and Chaetoceros muelleri was supplied daily. Four conditioning periods (14, 28, 45 and 60 days) with four replicates were used. On the day of collection and at the end of each conditioning period, clams were induced to spawn with thermal shocks (16.7 °C to 26 °C) and sperm. The first spawns were observed on day 28, but only 50% of the males and 33% of the females were mature, and their mean oocyte diameter (36.33 µm) was smaller than the minimum (45–50 µm) considered for ready-to-spawn clams. However, on day 45, all males and females were mature (mean oocyte diameter = 45.14 µm) and 1102 × 103 eggs were released. To ensure a high maturity rate, yellow clams should be conditioned in captivity for 45 days. Monitoring gonadal development in the wild to collect clams at advanced stages of gonadal development may be a less expensive strategy worth considering.

Fishes doi: 10.3390/fishes11040197

Authors: Jinhui Wu Xiaoxiao Zhang Qinguo Song Feifei Huang Tinghua Li Zhendong Qin Li Lin Fei Shi Huifan Liu Cuiyun Zou

Water-soluble pectin (WSP) is a soluble dietary fiber with a high esterification degree and certain viscosity and emulsifying properties. It has diverse bioactivities—including antioxidant, anticancer, and anti-inflammatory properties. This study aimed to investigate the in vitro antioxidant mechanisms of water-soluble pectin, and the in vivo effects of intestinal antioxidant capacity and gut microbiota composition in hybrid grouper (Epinephelus lanceolatus♂ × Epinephelus fuscoguttatus♀). In an experiment involving feeding fish with WSP added to the diet, the addition of 600 mg/kg WSP promoted the activities of CAT, SOD, and GSH-Px in the grouper intestinal tract, thereby enhancing the antioxidant properties. At the phylum level, the relative abundance of Actinomycetes and Armatimonadetes decreased significantly. At the genus level, the relative abundance of Vibrio and Subdoligranulum increased significantly. In addition, antioxidant genes, inflammatory factor genes, immune genes, apoptosis genes, and genes of specific transmembrane proteins may participate in the regulation and improvement of the hybrid grouper intestinal tract. (CAT, MnSOD, and GPX), (TNF-α, IL-β, IL-6, and TGF-β), (MHC2, TLR3, KEAP1, and IKK-α), (C3, C8, C9, and P53), and (Claudin-3a, Occludin, ZO-1, and ZO-3) may regulate the intestinal function of hybrid grouper. Therefore, adding an appropriate volume of WSP to the diet is beneficial for the intestinal health of hybrid groupers.

Fishes doi: 10.3390/fishes11040198

Authors: Ewen McLean Sofea Smith Ford Brodeur Frederic T. Barrows

Research designed to reduce or eliminate fishmeal (FM) in trout feeds, for reasons that have changed over time, has been conducted for over a century. Reducing the dependency on FM remains one of the most urgent issues facing the industry. Feed represents the most expensive operational cost of fed aquaculture, and is responsible for ecosystem disturbance following nutrient discharges. Rainbow trout, the second most farmed salmonid globally, can be raised completely without FM or fish oil (FO), with its growth and efficiency not differing from trout fed FM-based feeds. However, ingredient choice and nutrient supplementation strongly influence physiological responses, efficiency, and long-term outcomes. As land animal proteins are increasingly used in place of FM, both with and void of dietary FO, their distinct biological effects warrant focused evaluation. Although numerous studies have synthesized findings across various alternative protein categories including those with insect proteins and animal by-products, this literature is widely disseminated and sometimes difficult to access. The present contribution focuses on terrestrial/aerial animal proteins that have been used to totally replace FM in rainbow trout feeds. Attention is given to their effects on physiological control processes that may influence production efficiency. Areas worthy of future study are identified and include long-term performance and health dynamics, the refinement of nutritional and formulation strategies, and the broader evaluation of biological interactions and system-level outcomes.

Fishes doi: 10.3390/fishes11040196

Authors: Slavica Čolak Tomislav Šarić Matko Kolega Danijel Mejdandžić Relja Beck Perla Tedesco Marialetizia Fioravanti Andrea Gustinelli Monica Caffara

Parasitic diseases pose significant challenges to the success of mariculture. The health management strategies used in sea-cage aquaculture are not completely effective at preventing parasites from entering through interactions with wild fish. This study monitored the health status of greater amberjack (Seriola dumerili, Risso 1810) over a two-month period following their introduction to the farm in the Middle Eastern Adriatic Sea in July 2019. Zeuxapta seriolae was detected on the gills after 722 degree days (DD), with a 28% prevalence, a mean abundance of 1.00 parasite per fish (four examined arches), and a mean intensity of 3.57 parasites per infected fish. From 985 DD, prevalence was 100%; the parasite burden continued to rise, and by the final sampling at 1535 DD, the mean abundance reached 212.68 parasites per fish (53.17 per gill arch). At that point, fish express a sudden loss of appetite; no external symptoms were observed, except for mortality. This is the first report of Z. seriolae in cultured greater amberjack in the Adriatic Sea, and the study emphasises the difficulties in applying effective biosecurity measures in floating net cages.

Fishes doi: 10.3390/fishes11040195

Authors: Hongrui Chen Mingjie Liu Yu Sun Minghua Sun Zhifeng Gu Yi Yang

This study aimed to assess the species diversity and genetic structure of Meretrix clams around Hainan Island using mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding. The genus Meretrix is a common and economically important group of bivalves in the intertidal zones of Hainan Island, widely distributed in estuarine and nearshore sandy habitats and playing a significant role in local fisheries and aquaculture. In recent years, studies on Meretrix in Hainan have mainly focused on morphological identification and species records from limited coastal areas; however, due to the high phenotypic plasticity of shell morphology and the relatively subtle differences among species, traditional morphology-based identification remains challenging. Meanwhile, molecular systematic investigations of Meretrix in Hainan are still limited, particularly systematic studies using DNA barcoding to assess species diversity and geographic distribution patterns. A total of 141 individuals were collected from ten intertidal sites. Four species were identified—M. lyrata, M. lamarckii, M. meretrix and M. petechialis—with interspecific genetic distances (17.6–22.7%) far exceeding intraspecific variation (0.3–0.9%). Phylogenetic analysis based on COI sequences clearly distinguished four Meretrix species from the waters around Hainan Island, with each species forming a well-supported monophyletic clade, supporting their status as independent evolutionary lineages. In addition, two markedly divergent genetic lineages were detected within M. petechialis, suggesting that this species may possess a relatively complex population structure, one of which is typically found in northern Chinese waters, suggesting possible human-mediated introduction. Species richness was higher on the eastern coast, potentially influenced by regional hydrodynamic conditions. This study provides baseline DNA barcode data for Meretrix species in Hainan and supports the need for integrative management of this economically important resource.

Fishes doi: 10.3390/fishes11040194

Authors: Yanjun Shen

Globally, aquatic ecosystems are facing unprecedented and multifaceted pressures [...]

Fishes doi: 10.3390/fishes11040193

Authors: Joseph T. Eastman Mario La Mesa Richard R. Eakin

The single mental barbel is a distinctive feature of the benthic Antarctic fishes of the «cryonotothenioid» subfamily Artedidraconinae. These barbels are unusual because their primary sensory modality is tactility, not chemosensation as in most other teleosts. They also exhibit considerable interspecific and intraspecific variation in length and in the appearance of the terminal expansion and its epidermis. Barbels range from short to long and the terminal expansion can be nonexistent, small and round, or large and oblong. In most species, the epidermal surface of the terminal expansion exhibits projections of various shapes and sizes. These range from smooth and furrowed, to ridged and furrowed, to pointed, to palmate (having lobes originating from a common point), and to fringed and leaf-like. Barbels are also subject to intraspecific variation among the species in the genera Dolloidraco, Histiodraco, Artedidraco and Pogonophryne. The various epidermal surface patterns all increase the sensory surface area exposed to the substrate and may enhance detection of their prey, primarily polychaetes. They also enhance surface roughness of the epidermis, thereby dissipating mechanical forces and providing some protection from abrasion by the substrate. The various patterns are likely an epigenetic response to different local conditions of the substrate. This variation warrants caution in their use as a defining taxonomic character.

Fishes doi: 10.3390/fishes11040192

Authors: Selahattin Barış Çay Onur Obut Yusuf Ulaş Çınar Mehmet Ali Balcı Tuana Öğretici Cem Dalyan Fatih Dikmen Yakup Bakır Vahap Eldem

Sex determination in teleost fishes exhibits remarkable evolutionary plasticity; however, the underlying mechanisms remain largely elusive for many species of high economic importance. Herein, we provide the first genome-wide investigation of the genetic basis of sex determination in the European anchovy (Engraulis encrasicolus), an ecologically and commercially vital clupeiform fish. Using low-pass whole-genome resequencing of 100 sexually mature individuals (50 females and 50 males), we conducted a genome-wide association study (GWAS) and FST scans to identify sex-linked loci and characterize sex-determining regions (SDRs). Our analyses revealed two major candidate SDRs located on chromosomes 14 and 18, encompassing multiple sex-associated single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Among these, the amhr2 (anti-Müllerian hormone type 2 receptor) gene on Chr14 displayed the strongest and most consistent association with phenotypic sex, marked by several male-specific missense SNPs and InDel variants. Comparative and transcriptomic analyses confirmed sex-biased expression of amhr2 and other SDR-linked genes, potentially indicating a male heterogametic (XY-like) genetic sex determination system. These results provide the first molecular evidence for a candidate SDR in E. encrasicolus, raise the possibility of involvement of amhr2 and additional loci in sex determination, and highlight rapid sex chromosome turnover within Clupeiformes. Our findings not only expand the understanding of teleost sex determination evolution but also establish a genomic foundation for developing molecular tools for sex identification and population management in anchovy fisheries.