Fishes doi: 10.3390/fishes11100570

Authors: Qinglian Hou Zhiqiang Xu

Reliable wall-relative localization is required for robotic cleaning of aquaculture-vessel bulkheads, where sensor availability changes across the air–water interface. A two-stage study separated measured dry-wall performance from a controlled evaluation of cross-medium estimation logic. In Stage I, five coordinate-estimation models (P0–P4) were evaluated at 23 non-initial control points on an 8 m × 4 m vertical steel wall. The hard-axis-constrained WO/IMU model P0 achieved an RMSE of 0.1806 m and a maximum error of 0.3818 m on the predominantly axis-aligned trajectories. In Stage II, five localization models (M1–M5) were evaluated over four prescribed scenarios and 400 paired software-in-the-loop realizations. All methods used the same simulated sensor streams and initial position; no reference-derived auxiliary velocity was supplied during estimation. Medium- and visual-quality adaptation reduced the 95th percentile of per-run maximum error from 0.5480 m for the fixed-parameter filter to 0.3756 m for M4 and reduced the 95th percentile of per-run maximum excess position jumps to approximately 0.151 m. M5 used encoder–IMU heading disagreement only to inflate process uncertainty and achieved an aggregate ATE-RMSE of 0.1024 m, which was practically indistinguishable from the 0.1028 m obtained by M4. Its remaining benefit was confined mainly to modest improvements in transition error and recovery behavior under prescribed slip. The results demonstrate estimator behavior in a measurement-informed feasibility study; synchronized tank and vessel experiments remain necessary.

Fishes doi: 10.3390/fishes11100569

Authors: Xinyi Cao Beibei Qin Ruizhong Wei Haihang Chen Tiaoyi Xiao Zhao Lv

Grass carp (Ctenopharyngodon idella) aquaculture faces significant challenges due to grass carp hemorrhagic disease, which is instigated by the grass carp reovirus (GCRV). A major contributor to the high mortality rates associated with this disease is an excessive inflammatory response. Autophagy contributes to host disease resistance partly through modulating inflammation, in which autophagy-related gene 5 (ATG5) serves as a core component. In this study, we generated an ATG5-edited cell model with biallelic frameshift mutations in C. idella kidney (CIK) cells using the CRISPR/Cas9 system. Transcriptome and qPCR analyses indicated that ATG5 gene editing significantly influenced multiple biological pathways, including oxidative phosphorylation, phagosome formation, and arachidonic acid metabolism, and altered the expression of inflammation-related genes such as IL-1β, IL-8, TNF-α, IL-10, and TGF-β in CIK cells during GCRV infection. Further investigations through Western blot and ubiquitination assays demonstrated that ATG5 gene editing led to a notable decrease in the LC3-II/LC3-I ratio in CIK cells, along with a buildup of pro-IL-1β protein. The overexpression of grass carp ATG5 and IL-1β in HEK-293T cells reduced the ubiquitination of grass carp pro-IL-1β, facilitating its accumulation. Collectively, our results indicate that grass carp ATG5 modulates the expression of multiple inflammatory mediators and may shape pro-IL-1β protein abundance in a ubiquitination-associated manner. This study provides insights into autophagy-linked inflammatory regulation underlying grass carp hemorrhagic disease.

Fishes doi: 10.3390/fishes11100568

Authors: Marco Shizuo Owatari Leonardo Castilho-Barros Maurício Laterça Martins José Luiz Pedreira Mouriño

If Recirculating Aquaculture Systems (RAS) are widely regarded as one of the most promising technologies for sustainable aquaculture, why has their commercial adoption remained relatively limited in countries such as Brazil? Despite the remarkable scientific progress achieved in RAS technology over the past decade, a significant gap remains between experimental advances and their widespread commercial implementation. Most published studies have focused on optimising individual system components, including biofiltration efficiency, water quality management, feeding strategies, functional additives, microbial communities, and fish performance under controlled experimental conditions. Although these studies have substantially advanced our understanding of RAS operation, relatively few have critically evaluated whether the reported technological improvements remain effective, economically viable, or operationally feasible when transferred to commercial production systems. Consequently, many innovations that demonstrate promising biological outcomes at laboratory or pilot scales have yet to be validated under the technical, economic, and logistical constraints faced by commercial aquaculture enterprises. The Brazilian evidence indicates a heterogeneous but increasingly mature scientific landscape. Shrimp production provides relatively strong evidence for intensive RAS, biofloc, low-water-exchange, and integrated systems, whereas marine fish and mollusc production remains more strongly concentrated on experimental and pilot-scale optimisation. The future of RAS will not depend solely on further technological innovation, but on the successful integration of biological performance, engineering efficiency, economic feasibility, and practical scalability into commercially viable production systems.

Fishes doi: 10.3390/fishes11100567

Authors: Yizhu Chen Zhiqiang Wu Youcun Zou Zhiyuan Fu Li Wang Liangliang Huang Yangyang Zhang Yuzhen Peng

Accurate identification of early-life fishes (eggs and larvae) is important for understanding recruitment and supporting fisheries management in regulated rivers. We monitored early-life fish assemblages in the Xunjiang reach of the midstream Xijiang River during May–August in 2024 and 2025 after the Datengxia Water Conservancy Project began operating, collecting 97,934 specimens. Stratified cytochrome c oxidase subunit I (COI) DNA barcoding yielded 2960 high-quality sequences (98.27% success rate), resolving 69 taxonomic units across 52 genera and 14 families, with a representative sequence subset audited using maximum-likelihood and Bayesian inference phylogenies. Cyprinidae accounted for 92.30% of the analyzed barcodes, with Squaliobarbus curriculus frequently represented. The survey recorded all Four Major Chinese Carps, Elopichthys bambusa, Ochetobius elongatus, and rheophilic benthic fishes such as Garra orientalis and Sinogastromyzon wui. Early-life stages of Cirrhinus mrigala, Labeo gonius and tilapias were also detected. Volume-standardized generalized additive models of the 2025 field counts showed associations of egg and larval densities with discharge and pronounced nonlinear seasonality for larvae. These findings provide monitoring data for fishery resource management and ecological flow assessment in the midstream Xijiang River.

Fishes doi: 10.3390/fishes11100566

Authors: Xin Liu Dong Zhang Jörg Detlef Hardege

Waterborne chemical cues mediate reproductive interactions in decapod crustaceans, but interspecific variation in these cues remains poorly characterized. We compared behavioral responses and exploratory chromatographic profiles among four Lysmata species with contrasting social organizations: L. amboinensis, L. boggessi, L. debelius, and L. pederseni. Intermolt euhermaphrodite-phase (EP) focal shrimp were tested with conspecific and heterospecific postmolt EP-conditioned water, uridine-5′-triphosphate (UTP), uridine-5′-diphosphate (UDP), and seawater control. Conspecific conditioned water generally elicited the strongest responses, whereas response magnitude and type differed among species. UTP elicited the defined approach and follow response only in L. boggessi. UDP elicited no behavioral response in any species. Exploratory HPLC of one pooled composite conditioned-water sample per species revealed peaks at 17.01 and 24.29 min, with retention characteristics consistent with UDP and UTP standards, respectively. Two additional peaks at approximately 30.81 and 41.10 min were visually apparent in the pooled chromatograms of L. amboinensis, L. debelius, and L. pederseni. These results demonstrate interspecific differences in behavioral responsiveness and identify chromatographic features that warrant future testing with structural chemical identification.

Fishes doi: 10.3390/fishes11100565

Authors: Yuanyang Wang Junjun Tan Lei Chen Junjian Sun Senfan Ke Giri Kattel Xiaotao Shi

River fragmentation caused by hydropower development disrupts fish migration and threatens freshwater biodiversity worldwide. Fishways are widely used to restore connectivity, yet their effectiveness often varies among species due to differences in swimming ability and behavior responses to hydraulic conditions. This study evaluated a combined vertical slot–submerged notch with bottom orifice (VS–SNBO) fishway using laboratory experiments with two cyprinid species (Ctenopharyngodon idella and Opsariichthys bidens). We quantified hydraulic characteristics (velocity, turbulent kinetic energy, and strain rate), fish movement behavior, route selection, passage success, and energy expenditure. The VS–SNBO fishway achieved a overall passage success rate of 76.3% for both two cyprinid species. Among the successful upstream movement routes, 70.5% followed the vertical slot (VSL–VSL) route, despite higher velocities (0.60–0.83 m/s) and energy expenditure. Fish selectively utilized low-velocity zones near the orifice for recovery, indicating behavioral adaptation to heterogeneous flow conditions. Energetic analysis revealed trade-offs between passage efficiency and energy expenditure, with continuous movement routes reducing transit time but increasing metabolic demand. The combined fishway design provided multiple kinds of movement routes for different species to enable flexible movement strategies. These findings highlight that the VS–SNBO fishway can offer diverse hydraulics for multiple species and provide insights into how fish adjust their movement strategies in response to variable hydraulic conditions, and provide practical guidance for improving multi-species fish passage in regulated river systems.

Fishes doi: 10.3390/fishes11100564

Authors: Gabriel Dutra Rodrigues Vanessa Martins da Rocha Ulysses da Silva Palma Sabrina Lara da Luz Domickson Silva Costa Marco Shizuo Owatari Aline Brum Figueredo Ruschel Vinicius Ronzani Cerqueira Caio Magnotti

The use of residual biomass from industrial seaweed processing in aquafeeds may represent a potential route for the reuse of residual biomass within a circular-economy framework. This proof-of-concept trial evaluated the effects of dietary supplementation with wet solid residue from the seaweed Kappaphycus alvarezii in Mugil liza over 80 days under a mixed-feeding system. The treatments comprised nominal wet-residue levels corresponding to 0, 6, 12, 18, 24 and 30% of the reference daily feed intake, equivalent to 0, 0.7, 1.5, 2.2, 2.9 and 3.5% of the dietary mixture on a dry-matter basis, respectively. No mortality occurred, indicating no detectable adverse effects under the tested conditions. Haematological data indicated a pattern consistent with hormesis, with the 6% and 12% nominal wet-residue levels associated with increased erythropoietic responses. Intestinal integrity and fillet nutritional quality were preserved; however, eviscerated yield showed numerical variation among treatments, with the lowest median value observed at 18%. The mixed-feeding strategy allowed a reduction in commercial feed input without compromising growth. Overall, the tested nominal wet-residue levels, corresponding to 0.7–3.5% of the dietary mixture on a dry-matter basis, were not associated with detectable impairment of survival, intestinal integrity or fillet quality. Future studies should employ randomized designs with replicated experimental units to further explore the potential of using K. alvarezii processing residue as a partial replacement for traditional feed components in M. liza production.

Fishes doi: 10.3390/fishes11100563

Authors: Shinhyuk Hwang Sukkyoung Lee Kyungwon Cho Junsung Hur Sungyoon Cho

This study proposes an unsupervised image-processing method for segmenting the visible area occupied by adult flatfish (Paralichthys olivaceus) from standard red–green–blue (RGB) closed-circuit television (CCTV) images and quantifying visible areal occupancy. Rather than separating individual fish, the method treats the visible flatfish population as a unified segmentation target. To address surface reflections, wave-induced distortion, and illumination variation, the pipeline combines hue–saturation–value (HSV) saturation enhancement, lightness smoothing in the International Commission on Illumination L*a*b* (CIELAB) color space, K-means clustering, and morphological postprocessing. Evaluation of 15 randomly selected, manually annotated frames from three commercial farms in Jeju, South Korea, yielded a mean intersection over union (IoU) of 84.27 ± 4.11% and a Dice coefficient of 91.41 ± 2.45% (mean ± between-frame standard deviation). The proposed method had the highest overall mean agreement among the evaluated methods, including a preprocessed Gaussian mixture model (GMM), adaptive thresholding, Otsu binarization, and an all-tank baseline. However, GMM achieved higher IoU on four frames, and the all-tank baseline exceeded the proposed method in C05. Visible areal occupancy represents the two-dimensional proportion of the tank image occupied by the segmented region and serves as a relative indicator of stocking condition, not a direct measure of fish number, biomass, or volumetric stocking density. The method requires neither labeled model-training data nor additional sensing hardware.

Fishes doi: 10.3390/fishes11100562

Authors: Jiaxin Zhu Bowen Yan Geng Chen Zhaoshou Ran Jilin Xu

Palmitic acid (PA) is the most abundant saturated fatty acid in the diet of marine bivalves, yet its cellular regulatory mechanisms remain unclear. Using primary adherent mantle cells from the razor clam Sinonovacula constricta, we examined PA-induced lipid droplet (LD) accumulation and the underlying transcriptomic responses. We established that L-15 medium supplemented with 10% FBS provided optimal culture conditions. Oil Red O staining demonstrated that PA triggered a dose-dependent increase in LD content, with significant deposition evident at 50 μM. Transcriptomic profiling revealed 885 differentially expressed genes (477 up- and 408 downregulated), primarily enriched for lipid metabolism (e.g., PPAR and glycerophospholipid pathways), ER stress responses (e.g., protein processing and autophagy), and cytoskeletal organization. PA treatment was associated with upregulation of PLIN2, SCD, and HMGCS1 and downregulation of the fatty acid oxidation gene FABP3, suggesting a transcriptional shift toward lipid storage and reduced fatty acid oxidation. Concomitantly, PA may activate the ER stress response, as suggested by the dramatic induction of HSPA5, EIF2AK3, and DNAJC3. Our findings provide cellular evidence in bivalves that PA is associated with LD accumulation, potentially through integrated transcriptional changes in lipid metabolic and ER stress pathways, offering a reference for nutritional regulation strategies in S. constricta aquaculture. However, the causal relationships between these transcriptional changes and functional outcomes require further validation through protein-level and in vivo studies.

Fishes doi: 10.3390/fishes11100561

Authors: Shengping Li Shun Zhou Jing Dong Xiaohui Ai

The increasing occurrence of antibiotic-resistant bacteria has led to a shift in focus, with disinfectants becoming the primary alternative to antibiotics for prevention. Potassium persulfate compound (KMPS) has attracted extensive attention from consumers and is frequently used around the world, especially in aquaculture. However, the safety of KMPS is rarely reported. Here, this study evaluated the safety of KMPS in aquaculture, including its effects on water quality, bacterial eradication, microbial community diversity, and acute toxicity against Nile tilapia. The results show that KMPS (3.125, 6.25, and 12.5 μg/mL) had no role in water quality parameters, while it had a significant killing effect on BHI-cultured bacteria in pond water; microbial structure analysis demonstrated that KMPS (6.25 μg/mL) had no role in microbial community diversity, but several significantly different microbial communities and functions also existed and may even involve the eutrophication of pond water and enrich the abundance of drug-resistant microbial communities. Moreover, the 24-, 48-, and 72-h LC50 values of KMPS against Nile tilapia were illustrated, and high concentrations of KMPS could damage fish tissues. Therefore, this study will provide some useful reference values for researchers and fish farmers.

Fishes doi: 10.3390/fishes11100560

Authors: Ying Chen Sheng Zhang Kianann Tan Feilong Mo Kang Liu Xueyu Yan Lingjing Wei

This study assessed muscle quality and nutritional components of farmed Siganus fuscescens (rabbitfish) from Hepu, Qinnan and Tieshangang in Guangxi, China. Proximate nutrients, amino acids and fatty acids in fish muscle were determined. Qinnan samples had higher moisture and crude protein but lower ash content. Glutamic and aspartic acids dominated detected amino acids. The ratios of essential amino acids to total amino acids (EAA/TAA) and to non-essential amino acids (EAA/NEAA) ranged from 35.63 to 36.16% and 68.47 to 69.33%, respectively. Qinnan fish possessed the highest contents of total amino acids (TAA), essential amino acids (EAA), flavor amino acids (FAA), and the highest essential amino acid index (EAAI), indicating superior protein quality. The fatty acid profiles revealed that saturated fatty acids (SFA), monounsaturated fatty acids (MUFA), and polyunsaturated fatty acids (PUFA) each constituted more than 20% of the total fatty acids. Moreover, fish from Tieshangang were particularly rich in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Obvious regional nutritional differences existed in cultured rabbitfish. This work provides references for its quality assessment, resource utilization and targeted feed development.

Fishes doi: 10.3390/fishes11100559

Authors: Mu Ding Xiaohua Huang Gen Li Yu Hu Hangfei Liu Qingsong Hu Xinting Chen

Accurate underwater fish perception is a prerequisite for intelligent aquaculture, providing essential support for automated growth monitoring and precision feeding. Nevertheless, underwater imaging is severely affected by light scattering and cluttered backgrounds, making reliable fish perception and image-based non-contact fish size estimation particularly challenging. To overcome these limitations, this paper presents a geometry-aware underwater fish perception framework based on YOLOv5 for simultaneous object detection, pose estimation, and fish body size measurement. The proposed framework incorporates a Fish Geometry Coordinate Attention (FGCA) module into the backbone to enhance geometric feature representation by jointly modeling horizontal and vertical spatial dependencies, thereby improving the discrimination of elongated fish structures. In addition, a Dynamic Edge Relation Modeling (DERM) module is integrated into the neck to explicitly capture edge cues and structural relationships among key body regions, leading to more robust feature aggregation and more accurate key point localization under complex underwater conditions. Based on the predicted key points, the length and width of the fish can be estimated in a non-contact manner. Experimental results on a public underwater fish dataset demonstrate that the proposed framework achieves a Box mAP0.5 of 93.07% and a Pose mAP0.5 of 93.10%, consistently outperforming several representative YOLO-based detectors. Moreover, the proposed method maintains low body size estimation errors across different fish size categories. These results indicate that the proposed framework provides an accurate and practical solution for integrated underwater fish perception and image-based non-contact fish size estimation, offering significant potential for intelligent aquaculture and automated fish growth monitoring.

Fishes doi: 10.3390/fishes11090558

Authors: Ioannis C. Kilitzidis Maria Kamilari Orestis Anagnopoulos Nikos Bourdaniotis John A. Theodorou

Invasive non-indigenous species (NIS) are impacting Mediterranean coastal ecosystems, presenting ecological and economic management challenges. This study evaluates the economic viability of processing biomass from wild removals of the NIS pearl oyster, Pinctada radiata (Leach, 1814), into value-added seafood products in Greece. The study explored four product formats under two funding scenarios (Scenario A, full private financing; and Scenario B, 60% public co-financing): frozen, vacuum-packed raw oyster meat; frozen, vacuum-packed, breaded raw oyster meat; steamed, brine-smoked, vacuum-packed oyster meat; and steamed oyster meat preserved in olive oil and Mediterranean herbs. In Scenario A, with full private financing, the cumulative net cash flow (NCF) over five years was €165,402.78, with a profitability index (PI) of 2.93 and a payback period (PP) of 1.71 years. In Scenario B, with 60% public co-financing, the owner’s contribution reduced to €34,320.00. At the same time, the annual after-tax cash flow reached €50,240.56, resulting in a five-year cumulative NCF of €216,882.78, a PI of 7.32, and a PP of 0.68 years. These findings indicate that utilizing biomass from wild removals can be a financially viable strategy for managing NIS. This approach focuses on removal rather than aquaculture or translocation of P. radiata and emphasizes the need for adaptive governance and biodiversity protection to ensure effective population control. The study proposes a replicable bioeconomic model for integrating invasive biomass removal with value-added seafood processing in Mediterranean coastal regions.

Fishes doi: 10.3390/fishes11090557

Authors: Xin Luo Yadong Xie Wei Zhang Yuanyuan Dai Lin Ma Yu Wang Qikang Bo Zhongzhi Chen Jufeng Jiang

Tiger barb (Puntigrus tetrazona) is an economically important ornamental cyprinid widely cultured in the global aquarium trade; however, comprehensive information on its early development and reproductive performance remains limited. This study characterized embryonic development, larval and juvenile ontogeny, and reproductive performance under controlled hatchery conditions. Fertilized eggs were continuously observed from fertilization to hatching using stereomicroscopy, while larval development was monitored from hatching to 30 days post-hatching (dph). Reproductive performance was evaluated across five consecutive spawning cycles by determining estimated mean egg production per stocked female, fertilization rate, hatching rate, and larval survival. At 26.5–27.5 °C, embryonic development progressed through cleavage, blastula, gastrula, neurula, and organogenesis, and hatching commenced at 25 h 10 min post-fertilization; approximately 50% of viable embryos had hatched by 27 h 17 min, and hatching was completed by approximately 35 h 28 min. Newly hatched larvae measured 3.88 ± 0.56 mm in total length, and complete yolk-sac absorption occurred at approximately 7 dph. Characteristic vertical body pigmentation appeared at 15 dph, whereas juvenile characteristics were evident by approximately 20 dph, while complete scale coverage and adult-like coloration were observed by 30 dph. Reproductive performance declined significantly with successive spawning events, with fecundity decreasing from 182.33 ± 1.57 to 64.33 ± 3.52 eggs female−1 between the first and fifth spawnings, accompanied by reductions in fertilization, hatching, and larval survival rates. These findings provide a morphological developmental reference and practical hatchery benchmarks that can support broodstock management, larval rearing, and seed production of tiger barb in ornamental aquaculture.

Fishes doi: 10.3390/fishes11090556

Authors: Tian Wang Chen Yao Yongqiang Zhao Hui Huang Shuxian Hao Yanyan Wu Ya Wei Jianwei Cen

Oregano essential oil (OEO) was tested as a natural botanical anesthetic for spotted sea bass (Lateolabrax maculatus) through a comprehensive evaluation of anesthetic efficacy, physiological homeostasis, tissue integrity, flesh texture and carvacrol residual dynamics. Gradient treatments (100–300 µL/L) revealed dose-dependent anesthetic performance, and 200 µL/L was validated as the optimal dosage, under which fish reached deep anesthesia within 3 min and regained normal swimming within 5 min, with zero mortality recorded 12 h post-anesthesia. Temporary stress and oxidative stress fluctuations occurred in serum biochemistry and antioxidant enzyme profiles, which approached control levels after 12 h depuration. Only slight histological changes appeared in liver and gill tissues without permanent pathological damage. Minor declines in partial texture attributes recovered completely within 12 h, whereas other muscle quality indicators remained unaffected. Carvacrol was detected in muscle immediately after OEO anesthesia but was below the detection limit at all subsequent sampling times. Functioning as an efficient natural anesthetic with minimal physiological disturbance, OEO shows potential as an alternative to synthetic anesthetics for spotted sea bass live transportation and delivers dependable technical guidance for aquaculture production.

Fishes doi: 10.3390/fishes11090555

Authors: Levent Bat Gökhan Yıldız Ayşah Öztekin İshak Gençbay

In this study, the concentrations of thirteen trace elements (aluminum (Al), arsenic (As), cadmium (Cd), chromium (Cr), cobalt (Co), copper (Cu), iron (Fe), lead (Pb), manganese (Mn), mercury (Hg), nickel (Ni), selenium (Se), and zinc (Zn)) were determined in the edible muscle tissues of three commonly consumed fish species (Oncorhynchus mykiss, Dicentrarchus labrax, and Sparus aurata). Specimens were obtained from farmed stocks harvested and delivered to fish markets in Sinop, Türkiye, on the day of collection, with sampling carried out on a monthly basis throughout April, May, and June 2024. Zinc and iron exhibited the highest concentrations across all species, while toxic trace elements remained at notably low levels, with Cd (0.005–0.006 mg/kg), Hg (0.015–0.018 mg/kg), and Pb (0.010–0.011 mg/kg) remaining strictly below the European Union maximum permissible limits of 0.05, 0.5, and 0.3 mg/kg, respectively. In addition, a comprehensive human health risk assessment was performed based on a mean daily per capita fish consumption of 19.72 g. The Target Hazard Quotient (THQ) for all evaluated elements and the cumulative Hazard Index (HI), which ranged from 0.0794 to 0.0818 across species, were well below 1.0, indicating negligible non-carcinogenic risk. Carcinogenic risks, evaluated via the Risk Index (RI), were negligible for Cr (1.35–2.35 × 10−7) and well within acceptable bounds for iAs (2.77–4.13 × 10−6). The quantitative outcomes of this investigation suggest that under the evaluated conditions, trace element concentrations in these aquaculture products remain within safe baseline levels, contributing meaningful data on food safety and ecological monitoring within the southern Black Sea region.

Fishes doi: 10.3390/fishes11090553

Authors: Shaoyu Yang Xiaohui Cai Jingzhen Wang Mingzhong Liang

The efficient expression of recombinant proteins in aquaculture fish poses a significant challenge, partly due to the lack of dedicated bioinformatics tools for species-specific codon usage analysis and optimization. RiboScan (v1.0.0), a portable, single-file command-line tool executed in Python, was designed in this study, for mRNA codon diagnostics and optimization. RiboScan supports ten species, including five major aquaculture fish. High-risk windows that are computationally predicted to impair translational efficiency are identified based on two complementary metrics, namely, the Relative Adaptiveness Index (RAI) and estimated NN-based stability score, which are calculated using a sliding-window approach. An optimization module is used to replace the suboptimal codons in high-risk regions with host-specific synonymous codons, which are selected based on their high RAI values, leaving the encoded protein sequence unaltered. The efficacy of RiboScan was evaluated using coding sequences (CDSs) from three representative aquaculture fish genes, namely, Salmo salar growth hormone (gh; GenBank accession: M21573), Oreochromis niloticus interleukin-1 beta (il1b; GenBank accession: OR432591), and Ctenopharyngodon idella beta-actin (actb; GenBank accession: M25013). The tool identified 25–30 high-risk windows per CDS pre-optimization, whereas no high-risk windows were detected in any of the CDSs post-optimization. The mean RAI for Sal. salar gh, Or. niloticus il1b, and Ct. idella actb increased from 0.189 to 0.339, 0.126 to 0.270, and 0.140 to 0.231, respectively. RiboScan’s main analytical workflow requires no third-party dependencies, as it uses only the Python standard library. In addition, the tool yields publication-ready figures and structured comma-separated values (CSV) output files. RiboScan can be used to perform species-specific codon optimization for major aquaculture fish, and provides a practical computational framework for designing recombinant proteins, vaccines, and other engineered genetic constructs, thus contributing to aquaculture biotechnology research.

Fishes doi: 10.3390/fishes11090554

Authors: Shaoyu Yang Jing Fang Xiaohui Cai Jingzhen Wang

Simple sequence repeats (SSRs) are fundamental molecular markers in aquaculture genetics. Most existing SSR mining tools, however, were built for general-purpose use and apply identical detection criteria regardless of the organism, thereby overlooking the distinct genomic features of aquaculture species. Crustacean genomes, for example, are extremely AT-rich, while bivalve genomes show exceptionally high SSR density. Conventional tools account for neither feature. Here, we present AquaSSR, a lightweight SSR analysis tool that implements taxon-specific mining rules and primer design parameters tailored to three major taxonomic groups in aquaculture: bony fish, crustaceans, and bivalve mollusks. AquaSSR adopts an aquaculture-oriented screening strategy that excludes mononucleotide repeats (a methodological choice suited to conventional genotyping platforms), applies a three-tier dinucleotide threshold adapted to each group’s genome composition (≥6 for fish, ≥8 for AT-rich crustaceans, ≥7 for high-density bivalves), and optimizes primer GC scoring centers for taxon-specific base composition. The complete pipeline, from FASTA input through SSR detection, primer design, and optional in silico e-PCR validation to Excel and figure output, runs with a single command and requires only four pip-installable Python libraries, with no external command-line bioinformatics programs. Validation on transcriptome datasets of Larimichthys crocea (fish), Litopenaeus vannamei (crustacean), and Magallana gigas (bivalve) identified 8398, 5471, and 2287 SSR loci, respectively, demonstrating that the taxon-specific thresholds effectively shaped the motif composition profiles across species.

Fishes doi: 10.3390/fishes11090552

Authors: Gao Gao Jingnan Wei Lingyu Gan Huiying Wang Zixiang Ma Huizhen Yin Huixuan Xu Yizhu Deng Run Bi Baoliang Bi

The red swamp crayfish is cultivated in intensive ponds and integrated rice–crayfish systems, which drive distinct growth-oriented versus stress-resistance syndromes, yet their metabolic underpinnings are unclear. We applied untargeted LC-MS metabolomics to hepatopancreas from both systems. Among 2681 metabolites, 566 were differentially abundant. Pond-cultured crayfish exhibited a lipid-centric anabolic metabolome (enriched ceramides, lysophosphatidylcholines, and free fatty acids) that supports rapid growth but incurs oxidative stress. Conversely, rice-paddy crayfish showed enhanced purine metabolism, aminoacyl-tRNA biosynthesis, and D-amino acid metabolism, reflecting energy mobilization and protein turnover under limited resources. Targeted assays confirmed significantly higher GSH/GSSG ratios (11.29 vs. 5.07) and lower MDA (3.07 vs. 5.00 nmol/mL) in rice-paddy crayfish, validating transcriptomic upregulation of glutathione biosynthesis. Integration with transcriptomic and phenotypic data revealed coherent trait–metabolite modules. Our findings suggest a trade-off between biomass production and systemic stress resistance, mediated by differential activation of purine and glutathione pathways, consistent with a growth–defense trade-off framework. This provides a mechanistic framework for sustainable aquaculture: integrated systems enhance robustness, whereas ponds require strategies to mitigate physiological load.

Fishes doi: 10.3390/fishes11090551

Authors: Elena de la Roca José F. Ferrer Cinta López Alberto Vélez-Ruiz Marcelino Herrera

Anemonia viridis is an ecologically and commercially important sea anemone whose natural populations have declined due to overexploitation, climate change, and the expansion of the invasive alga Rugulopteryx okamurae. Therefore, the recovery of natural populations is necessary through the development and optimization of zootechnical techniques for rearing and maintaining sea anemones in captivity. This requires the identification of reliable indicators of physiological status, which remains poorly understood. This study evaluated the suitability of metabolic, antioxidant, and symbiosis-related parameters to assess the physiological status of A. viridis under two distinct experimental stress scenarios: acute aerial exposure (6 h) and prolonged starvation and darkness (10 days). Acute aerial exposure induced rapid metabolic adjustments, characterized by increased glucose and lactate concentrations, reduced superoxide dismutase activity, and unchanged glutathione peroxidase activity, with no significant changes in the measured symbiosis-related parameters. In contrast, prolonged starvation and darkness altered glucose and cholesterol levels and antioxidant responses, and was accompanied by numerical decreases in Symbiodiniaceae density and total chlorophyll a content normalized to host protein, although without reaching statistical significance. Thus, while the metabolic and antioxidant biomarkers revealed distinct physiological responses to the two experimental stress scenarios, evidence for changes in the cnidarian–Symbiodiniaceae symbiosis remained limited. Overall, the combined assessment of metabolic, antioxidant, and symbiosis-related biomarkers provided a more comprehensive evaluation of holobiont physiological status than individual biomarkers alone. This integrative biomarker panel represents a practical tool for optimizing rearing conditions and supporting the recovery of A. viridis.

Fishes doi: 10.3390/fishes11090550

Authors: Wenjie Peng Ming Li Lele Fu Ping Tan Jiuxian Yang Qian Li Aosi Zou Jingjie Feng

Sichuan taimen (Hucho bleekeri Kimura 1934) has experienced severe loss of spawning habitat due to hydropower development, as reservoir impoundment has inundated and altered the hydraulic conditions of its original riverine habitats, substantially reducing suitable habitats for its survival and reproduction. Identifying alternative spawning sites and creating suitable hydraulic conditions are therefore critical for this endangered species. Field investigations and literature synthesis identified key spawning requirements, including water velocity of 0.4–0.8 m s−1, water depth of 0.2–0.8 m, sand–gravel substrates with ≥60% sand and fine gravel, and water temperature of 4–10 °C. An integrated ecological engineering scheme combining gravel-bar construction, substrate reconstruction, hydraulic optimization, and nursery habitat enhancement was developed. A depth-averaged, 2-D, hydrodynamic–habitat model showed that restoration increased WUA during the spawning period from 5.2–6.5% to 39.5–47.6%, corresponding to a 70–287% increase, with WUA increasing to up to ~3.9 times the pre-restoration value. The results demonstrate that ecological engineering can effectively enhance spawning habitat under hydropower-regulated flows and provide a transferable framework for endemic rheophilic fishes in regulated alpine rivers.

Fishes doi: 10.3390/fishes11090549

Authors: Niki Milatou Odysseas Papadopoulos-Michalas Aikaterini Sakellari Sotirios Karavoltsos Persefoni Megalofonou

This study determined total mercury (THg) concentrations in the muscle tissue of Atlantic chub mackerel (Scomber colias) from the Saronic Gulf, evaluated temporal variation, and examined their relationship with biological parameters. THg was analyzed in 79 muscle samples, comprising 50 individual and 29 pooled samples derived from 179 Atlantic chub mackerel specimens, using cold vapor atomic absorption spectrometry (CVAAS). Method accuracy was verified by certified reference material analysis, with a mean recovery of 103%. THg concentrations ranged from 0.005 to 0.247 μg/g wet weight, with a mean value of 0.065 ± 0.053 μg/g. THg levels varied significantly among sampling periods, with the highest concentrations observed during the September sampling periods, particularly in September 2024. A strong positive correlation was found between THg concentration and fish size, both for fork length (p < 0.001) and dressed weight (p < 0.001), while a moderate positive association was also observed with Fulton’s condition factor (p < 0.001). All concentrations were below the European Union maximum permitted level for mercury in Scomber species (0.30 μg/g wet weight). Risk assessment indicated low concern at mean THg levels (HQ = 0.50), but potential concern under the maximum-exposure scenario (HQ = 1.9). These findings provide baseline data on THg contamination in Atlantic chub mackerel from the Saronic Gulf, demonstrate size-dependent THg accumulation, and contribute to the evaluation of its potential utility in mercury biomonitoring and seafood safety assessment.

Fishes doi: 10.3390/fishes11090548

Authors: Jiali Jin Lan Zhou Yachan Ji Changsong Wu Jing Zhang Jinping Wu Jinhua Gan Chuangju Li Rui Ruan

KDF (potassium diformate) has been recognized as a highly promising additive due to its beneficial effects on growth and immunity improvement. In order to expand the application of KDF in the aquatic farming practice, the effects of KDF on ricefield eels were thoroughly evaluated. In the present study, the growth performance, blood biochemistry, hepatic health and disease resistance were assessed in the juvenile ricefield eels fed diets supplemented with 0 (D0), 3 (D1), 6 (D2), 9 (D3), 12 (D4) and 15 (D5) g/kg KDF. After 8 weeks feeding, fish weight gain rate (WGR) was improved by KDF addition, and the estimated optimum dietary KDF was determined at 8.91 g/kg according to the regression analysis between dietary KDF level and WGR. Fish condition factor (CF) was increased by dietary KDF supplementation compared to the control (D0). The VSI of fish decreased significantly and then kept stable when the dietary KDF level was above 9 g/kg (p < 0.05). The supplementation of KDF in diet had no significant effect on the moisture, crude ash, and crude protein contents of the whole fish (p > 0.05), while the crude lipid content in the D4 group was significantly lower than that in the control (p < 0.05). Compared to the control group, the inclusion of 9 g/kg KDF (D3) in the diet significantly decreased serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT) (p < 0.05). Liver catalase (CAT) activity increased significantly with increasing the level of KDF in diet, but it remained stable at KDF levels at and above 9 g/kg (D3) (p < 0.05). The significant improvement of glutathione peroxidase (GSH-Px) activity and total antioxidant capacity (T-AOC) were found in the D1 and D4 groups, respectively (p < 0.05). Liver malondialdehyde (MDA) content showed a non-monotonic pattern across KDF levels, and the addition of KDF in diet did not significantly alter MDA content compared to the control (p > 0.05). Fish in the D4 group showed the lowest liver malondialdehyde (MDA) content. Serum ALP activity was markedly elevated in the D3 group compared with the control (p < 0.05). Supplementation of KDF in diets enhanced hepatic ALP and ACP activities, which differed significantly from the control in the D3 and D4 groups, respectively (p < 0.05). The histological results indicated that while no significant alteration of liver cell structure was observed, fish liver showed a lower number and size of lipid droplets with the KDF level increasing, and the hepatic sinusoids appeared more prominent in the high KDF group (D5). The Aeromonas hydrophila challenge test demonstrated that the addition of 9 g/kg KDF (D3) in fish diet significantly increased the survival rate of juvenile ricefield eel (p < 0.05). In summary, dietary supplementation with KDF significantly enhanced growth performance, improved several biomarkers associated hepatic health, and strengthened pathogen resistance in juvenile ricefield eels.

Fishes doi: 10.3390/fishes11090547

Authors: Lu Zhang Qinghui Ai Chunxiao Zhang Huitao Li Xiaoru Chen Haifeng Mi Li Cai Jie Chen Tao Teng

Vitamin D3 (VD3) plays a critical role in bone mineralization and growth in fish, yet its dietary requirement for large yellow croaker (Larimichthys crocea) remains unclear. This study aimed to determine the optimal VD3 level for growth performance and bone health in large yellow croaker. A 9-week feeding trial was conducted with juvenile large yellow croaker (6.16 ± 0.19 g) using six isonitrogenous and isoenergetic diets containing graded VD3 levels (measured: 32.7, 216.8, 392.5, 773.2, 1524.5, and 3071.6 IU kg−1). Growth indices (weight gain, specific growth rate, feed efficiency ratio, protein efficiency ratio) increased significantly (p < 0.05) when dietary VD3 rose from 32.7 to 392.5 IU kg−1, then plateaued. VD3 supplementation significantly affected hepatic VD3 content, whole-body ash, calcium, and phosphorus levels, and mineralization of vertebrae, opercula, and scales, as well as serum alkaline phosphatase, hydroxyproline, calcium, and inorganic phosphorus (p < 0.05). Based on a broken-line model using weight gain, the dietary VD3 requirement was estimated at 426.5 IU kg−1; using a quadratic model with hepatic VD3 content, the estimate was 2388.9 IU kg−1. Overall, appropriate dietary VD3 supplementation is essential to support optimal growth and bone mineralization of juvenile large yellow croaker. This finding provides a scientific basis for dietary VD3 recommendations to optimize growth and bone health in large yellow croaker, contributing to improved aquaculture productivity.

Fishes doi: 10.3390/fishes11090546

Authors: Fuyong Huang Qingyi Zhang Suiyang Shen Lina Jiang Jiahao Zhang Yangxin Dai Xiao Liang Jinyu Tang Lun Qian

This study evaluated the effects of partially or completely substituting fishmeal and fish oil with dried housefly (Musca domestica) maggots on the growth, nutritional composition, antioxidant capacity, and immunity of Chinese mitten crab (Eriocheir sinensis). An 8-week feeding trial was conducted using three isonitrogenous and isolipidic diets: T1, a control formulated feed containing 350 g/kg fishmeal and 40 g/kg fish oil; T2, a formulated feed containing 200 g/kg fishmeal and 29 g/kg fish oil, supplemented with 161 g/kg dried housefly maggots; and T3, a formulated feed containing no fishmeal and 15 g/kg fish oil, supplemented with 375 g/kg dried housefly maggots. The results showed that T2 maintained survival and growth comparable to the control while enhancing the HSI, EAA profiles, and n-3/n-6 ratio, along with elevated antioxidant capacities (CAT and GSH-Px) and lysozyme activity. In contrast, T3 increased the EAA, TAA, and EAA-related ratios, while elevating the BAA, atherogenic index and thrombogenic index, but reducing the beneficial PUFA and suppressing immune parameters. Notably, T3 did not induce excessive hepatopancreatic lipid accumulation. A mineral analysis revealed tissue-specific deposition patterns, with muscle accumulating K, Ca, Zn, Cr, and Cu, while the hepatopancreas retained a higher Ca, Fe, and Se. Despite the increased Cr and Cu accumulation with maggot inclusion, all levels remained within safety limits, posing no health risk to crabs. These findings demonstrate that dried housefly maggots represent a viable alternative protein and lipid source for crabs, with 161 g/kg being the preferable inclusion level among the two tested levels. Inclusion at 161 g/kg provides nutritional complementarity with the formulated feed and enhances the immune function, while inclusion at 375 g/kg disrupts the nutritional balance and immunological homeostasis. This study provides a scientific foundation for optimizing maggot-based feeding strategies in sustainable crustacean aquaculture.

Fishes doi: 10.3390/fishes11090545

Authors: Seonghun Kim Sena Baek Seokjin Yoon Youngil Seo

This study evaluated snow crab (Chionoecetes opilio) gillnet selectivity using the traditional Share Each Length’s Catch Total (SELECT) framework and a generalized additive model (GAM). Comparative fishing experiments were conducted in the East Sea of Korea using four stretched mesh sizes (210, 240, 255, and 270 mm). Among the candidate SELECT models, the binormal model had the lowest Akaike’s Information Criterion (AIC), although the normal and gamma models also received substantial support (ΔAIC < 2). Under the equal-fishing-power assumption, the ascending L50 increased from 70.47 mm for the 210 mm mesh to 90.60 mm for the 270 mm mesh, indicating a progressive shift in retention toward larger crabs across the tested gear configurations. The final GAM2 and the selected binormal SELECT model produced closely similar fitted selectivity patterns across most of the observed relative-size range and nearly identical in-sample agreement with the observed conditional catch proportions. However, the binormal components should not be interpreted as distinct biological capture mechanisms because capture behavior was not directly observed. Overall, the results support the complementary use of SELECT and GAM for evaluating snow crab gillnet selectivity, while acknowledging uncertainty associated with relative fishing power and the fixed panel arrangement.

Fishes doi: 10.3390/fishes11090544

Authors: Sabrina Vitória Ferreira da Costa Caio Augusto Perazza Micheli Zaminhan-Hassemer Leticia Rafaela de Morais Fernanda Loureiro de Almeida O’Sullivan Ze-Xia Gao Emily Bronze dos Santos Danillo Pinhal Eric Hallerman Alexandre Wagner Silva Hilsdorf

Intermuscular bones (IBs) are spicule-like, ossified structures located in the myosepta of muscles on either side of the vertebrae that are unique to several orders of teleost fishes, including Order Characiformes, for which research on the characteristics of IBs is limited. We investigated the morphologies and numbers of epineural and epipleural IBs in five characiform fishes: common wolffish/taíra Hoplias malabaricus (Family Erythrinidae), blackfin pacu/tambaqui Colossoma macropomum (Serrasalmidae), three-spot leporinus/piau-três-pintas Leporinus friderici (Anostomidae), flannel-mouthed characiform/grumatã Prochilodus vimboides (Prochilodontidae), and saguiru Cyphocharax modestus (Curimatidae). In addition, we characterized the ontogenetic formation of IBs in C. macropomum, examining cleared and stained juveniles at different developmental stages. The effects of species, intermuscular bone type, IB series, body side, and their interactions were assessed using a zero-inflated generalized linear model. The results revealed differences in the number, shape, and distribution of intermuscular bones (IBs) among species and morphological types. All seven previously reported types of IBs in characiforms were observed, along with three newly identified shapes. The total number of IBs ranged from 242 to 304 across the respective species. In juvenile C. macropomum, mineralized IBs were first detected at approximately 15 mm total length, after the main axial skeleton was already formed. Early IBs first appeared as simple elements and progressively acquired bifurcated morphologies during development, with “Y”-shaped IBs becoming evident in later juvenile stages.

Fishes doi: 10.3390/fishes11090543

Authors: Zhiyuan Xiang Wen Ma Juan Du Lixiong Yu Huatang Deng Xinbin Duan Mingdian Liu Xiping Yuan Huiwu Tian Lei Gao

Freshwater lakes worldwide are undergoing rapid degradation, raising concerns about the effectiveness of recent large-scale conservation interventions. China’s ‘10-year fishing ban’ represents one of the world’s most ambitious fishery moratoria, yet its ecosystem-level consequences remain poorly quantified. Using data from the two seasonal surveys conducted in Dongting Lake in 2019, we applied a mass-balanced Ecopath with Ecosim model to evaluate how fishing closure, and its combination with multi-species stock enhancement, affects trophic structure, energy flows, and system stability from 2021 to 2030. Simulations show that the closure-only scenario nearly doubles total ecosystem production, yet yields limited improvement in maturity indicators, reflecting a slow recovery of food web complexity. Across the tested closure-plus-enhancement scenarios, the highest projected system omnivory index occurred under scenario S5 (from 0.24 to 0.27), whereas the highest projected Shannon diversity index (from 0.59 to 0.64) and total transfer efficiency (from 10.80% to 11.12%) occurred under scenario S1, relative to the 2019 baseline. Based on the level-wise responses of the L9 treatments, a recommended combined scenario consisting of 1.04 t bighead carp, 4.30 t grass carp, and 1.14 t silver carp, with no additional black carp stocking, was constructed. Under this scenario, the model projected enhanced biomass recovery and a shorter restructuring period for key functional groups. Our study provides a reference for predicting ecosystem responses following the ‘10-year fishing ban’ and also provides data for ecosystem-based assessments for stock enhancement.

Fishes doi: 10.3390/fishes11090542

Authors: Jorge Andrés Zambrano Navarrete Luis Gustavo Tavares Braga

Arapaima gigas is a carnivorous freshwater species with high dietary protein requirements and increasing relevance for aquaculture. However, nutritional studies with this species frequently use experimental diets with varying carbohydrate fractions that are not explicitly controlled. Nitrogen-free extract (NFE), which represents soluble dietary carbohydrates, may therefore influence growth and digestibility responses and act as a confounding nutritional factor. The objective of this study was to evaluate the effects of dietary NFE on growth performance, feed efficiency, and nutrient utilization in A. gigas through meta-analysis. A systematic literature search was conducted using peer-reviewed and grey-literature sources. Studies were included when they provided quantitative information on dietary composition together with growth-performance indicators or digestibility coefficients. Twenty studies met the eligibility criteria and were included in the quantitative synthesis. Specific growth rate (SGR), feed conversion ratio (FCR), and apparent digestibility coefficients (ADC) of dry matter (DM), crude protein (CP), and gross energy (GE) were analysed using standardized mean differences (Hedges’ g) under random-effects models. Digestibility analyses were restricted to plant-based energetic and protein ingredients because animal-derived raw materials contribute minimal NFE. Higher dietary NFE levels were associated with reduced SGR, while the effect on FCR was more sensitive to study structure and within-study dependence. Higher NFE levels were also associated with reduced DM and GE digestibility, whereas the effect on CP digestibility was not statistically significant and showed substantial heterogeneity. Sensitivity analyses supported the robustness of the SGR, ADC DM, and ADC GE responses. The available evidence suggests that dietary NFE represents an important source of variation in nutritional studies involving A. gigas. Although heterogeneity among studies and variation in ingredient composition limit causal inference, improved control and reporting of dietary NFE may reduce confounding effects and improve interpretation of growth, feed efficiency, and digestibility responses in future feeding trials.

Fishes doi: 10.3390/fishes11090541

Authors: Zorana Kljaković-Gašpić Ankica Sekovanić Tatjana Orct Frano Matić Hrvoje Kalinić Ivan Župan Marijana Matek Sarić

This study examined the distribution of 24 metal(loid)s in muscle, liver, gills, and gonads of dominant fish species from Vrana Lake, Croatia. Element concentrations were determined by inductively coupled plasma mass spectrometry (ICP-MS). The effects of tissue type, species, fish size, and season were evaluated using classical statistics, principal component analysis (PCA), and the Neural Gas (NG) algorithm. Tissue type was the primary determinant of elemental composition. Concentrations of most elements were highest in liver and gills, intermediate in gonads, and lowest and most uniform in muscle. Species-related differences were generally limited, while size-related relationships were tissue- and species-dependent, with generally weak or negative trends in muscle and more variable responses in metabolically active organs. PCA revealed clear tissue-based structuring but comparatively limited separation among species. NG complemented these findings by providing additional resolution of within-tissue heterogeneity and low-frequency multielement profiles. Overall, our findings provide a baseline reference dataset for the biota of Vrana Lake, indicate tissue physiology as the main factor influencing elemental variability, and indicate that NG may serve as a useful complementary approach for exploring complex multielement biomonitoring data.

Fishes doi: 10.3390/fishes11090540

Authors: Xing Che Renyou Yang

Non-contact underwater fish counting supports stocking-density estimation and management in intelligent aquaculture. This study evaluated a 900-image annotated TV5/IOC in-domain dataset derived from the right-view stream of one source video. For each of three seed-controlled splits, 720 images were used for training and 180 for validation. All controlled configurations used the same raw single-view (Raw-SV) supervised and inference input. High-density-aware density modeling (HDA-DM) applies a mild sample weight only to the density loss of high-count training images. HDA-DM reduced the Main900 three-seed mean MAE from 4.024 ± 0.578 to 3.739 ± 0.414 (7.07%) and reduced the Hard200 challenging-case mean MAE from 9.799 ± 1.792 to 8.863 ± 0.304 (9.56%). The improvement was not identical in every seed. Cross-view density distillation (CVDD), evaluated as a training-only ablation, did not further improve HDA-DM: the combined configuration obtained 3.987 ± 0.635 on Main900 and 9.666 ± 1.373 on Hard200. A loss-scope audit further showed that the original density-only HDA-DM formulation outperformed weighting density, count, and shape supervision together. HDA-DM introduces no additional inference-stage parameters or operations. Because the evidence is limited to three seeds and one acquisition source, all comparisons are descriptive and no formal statistical-significance or external-generalization claim is made.

Fishes doi: 10.3390/fishes11090539

Authors: Maolian Li Xiaoming Yang Zhoujia Hua Jiangfeng Zhu

Understanding the spatial distribution patterns of pelagic species such as yellowfin tuna (Thunnus albacares) is essential for ecosystem-based fisheries management. However, characterizing CPUE–environment relationships remain challenging because these relationships may be nonlinear and spatially heterogeneous across large oceanic regions. To address these challenges, we developed an interpretable spatial modeling framework, geographically neural network weighted regression integrated with GeoShapley analysis (GNNWR-GeoShapley), which combines the nonlinear learning capability of neural networks with spatially explicit characterization and interpretation of model relationships. Using Pacific longline fishery data and multi-source environmental variables from 2004 to 2023, we constructed quarterly models of CPUE–environment relationships and compared the performance of GNNWR with Generalized additive model (GAM), geographically weighted regression (GWR), graph neural network (GNN) models, and Geographical Random Forest (GRF). The results demonstrated that GNNWR showed the best overall performance across seasons, effectively capturing nonlinear relationships and spatial heterogeneity in yellowfin tuna nominal CPUE. GeoShapley analysis further revealed that sea surface and subsurface (150 m) temperature and salinity were among the most important environmental variables associated with nominal CPUE variations. Nonlinear response patterns indicated that SST values above approximately 25 °C and T150 values above approximately 19 °C were associated with positive model contributions, whereas higher salinity values (>35) exhibited negative contributions. Moreover, spatial effects represented by the geographical location variable (GEO) and their interactions with environmental variables revealed pronounced spatial heterogeneity, with the contribution patterns of environmental factors varying across seasons and regions. This study provides an interpretable spatial modeling framework for characterizing complex species–environment relationships and offers new insights into the spatial variability of Pacific yellowfin tuna nominal CPUE for fisheries oceanography and sustainable resource management.

Fishes doi: 10.3390/fishes11090538

Authors: Ke Shao Meihua Xiong Ezhou Wang Le Hu Yanfu Que Xingkun Hu

Understanding how dams restructure fish diversity is critical for biodiversity conservation and reservoir management. Here, we integrated species, taxonomic, and functional diversity within a unified framework to assess fish community responses to the Datengxia Water Conservancy Project impoundment on the Hongshui River (Pearl River basin). Based on surveys before (2013) and after (2020–2022) impoundment across upstream, downstream, and tributary reaches, we recorded 162 species, including four nationally protected, four endangered, two critically endangered, and 19 exotic taxa. Our three-dimensional assessment uncovered three key patterns: (1) a marked community shift toward limnophilic and slow-flowing species, with three new dominants (Ptychidio jordani, Culter alburnus, and Oreochromis mossambicus) emerging, while rheophilic and migratory forms contracted; (2) trait-selective diversity losses—locomotion-related functional richness (FRic) declined substantially (up to 42.1% at Wuxuan), whereas feeding-related FRic increased markedly (up to 55.1% at Laibin), and reproduction-related traits exhibited stable compositional profiles (spring-dominated spawning, demersal-adhesive eggs) with heterogeneous index responses across sections; taxonomic diversity revealed closer taxonomic relatedness and structural imbalance; (3) a consistent spatial gradient (tributary > downstream > upstream), with downstream assemblages exhibited lower spatial variation in diversity indices. These community shifts were observed alongside habitat modification (lotic habitat shrinkage and fragmentation) and coincided with exotic invasions and over-dominance of resident species. These patterns should be interpreted as descriptive findings given the observational design. This three-dimensional assessment framework provides complementary insights for evaluating dam-related ecological impacts, generating testable hypotheses for future research and conservation planning.

Fishes doi: 10.3390/fishes11090537

Authors: Kyung Mi Lee Hyun-Mi Jung Seok-Ryel Kim

Species-specific hematological reference intervals and reliable blood biomarkers are essential for physiological health assessment and disease diagnosis in aquaculture, yet such information remains unavailable for cultured starry flounder (Platichthys stellatus). This study aimed to establish hematological and plasma biochemical reference intervals for cultured starry flounder under optimal culture conditions and to identify diagnostic biomarkers associated with high-temperature stress. A total of 124 clinically healthy sub-adult starry flounder (mean total length, 28.9 ± 0.3 cm; mean body weight, 402.2 ± 13.7 g) were investigated under low—(4.1–5.7 °C, n = 30), optimal—(16–19 °C, n = 62), and high-temperature (26–28 °C, n = 32) conditions. Thirteen hematological and plasma biochemical variables, including osmolality, calcium, magnesium, cortisol, heat shock protein 70 (HSP70), glucose, total cholesterol, total protein, immunoglobulin M (IgM), aspartate aminotransferase (AST), alkaline phosphatase (ALP), hemoglobin, and hematocrit, were analyzed. Reference intervals were established for fish maintained under optimal temperature following ASVCP recommendations. Significant differences were observed among temperature groups in most blood variables (p < 0.05). Plasma cortisol exhibited the highest diagnostic performance for discriminating high-temperature fish (AUC = 0.870), followed by osmolality (AUC = 0.812). Principal component analysis demonstrated distinct physiological responses among temperature groups, while Random Forest analysis identified cortisol and osmolality as the most influential variables, with ALP, total protein, and AST also contributing to discrimination between optimal- and high-temperature fish. HSP70 concentrations tended to increase under high-temperature conditions, although the difference among temperature groups was not statistically significant. These findings provide the first hematological reference intervals for cultured starry flounder and identify plasma cortisol as the biomarker with the highest diagnostic performance for detecting high-temperature stress under the conditions examined. The proposed reference intervals and diagnostic biomarkers provide a practical framework for physiological health assessment and early thermal stress monitoring in starry flounder aquaculture.

Fishes doi: 10.3390/fishes11090536

Authors: Bianca M. Neves Felippe A. Daros Rafael Schroeder Rafael G. Kulzer Marcus R. Costa Alberto T. Correia

Otolith shape has been widely used as a tool to investigate the population structure of marine fish, as it reflects environmental, physiological, and genetic influences throughout the lives of individuals. The morphological variability of Pomatomus saltatrix sagittal otoliths along the southeastern–southern coast of Brazil was assessed using Elliptic Fourier Descriptors (EFDs) and Wavelet Transform Descriptors (WTDs). A total of 74 individuals from Rio de Janeiro (RJ, N = 25), São Paulo (SP, N = 24), and Santa Catarina (SC, N = 25) were analyzed. The coefficients obtained from both methodologies were subjected to multivariate analyses, including Permutational Multivariate Analysis of Variance (PERMANOVA) and Flexible Discriminant Analysis (FDA), combined with Jackknife Cross-Validation (JKC). The results showed high similarity in otolith shape among the sampled locations. Overall, PERMANOVA detected significant spatial differences for both EFD and WTD, although the proportion of variation explained by sampling location was low for both descriptors (<5%). After Bonferroni correction, no pairwise differences remained significant for EFD, whereas WTD indicated significant differences between SC and the other two sampling locations. Nevertheless, FDA indicated partial discrimination among sampling sites, with some overlap among groups for both descriptors. Despite this, JKC rates were high, reaching 92% for EFD and 87% for WTD. Overall, the results point to a pattern of weak spatial structuring in P. saltatrix along the southeastern–southern coast of Brazil. Although subtle morphological heterogeneity was detected among the analyzed locations, the evidence does not support the existence of completely isolated stocks. The observed patterns indicate weak spatial phenotypic differentiation and may be consistent with population connectivity; however, connectivity cannot be directly inferred from otolith shape alone and represents only one possible interpretation, as similar environmental conditions, shared growth histories, or limited discriminatory power of otolith morphology could also contribute to the observed scenario. Thus, the study reinforces the utility of otolith morphometry as a complementary tool for population studies and highlights the importance of integrating it with other phenotypic and genotypic approaches for a more comprehensive understanding of the structure of the species’ stocks.

Fishes doi: 10.3390/fishes11090533

Authors: Yuanhao Ren Han Long Xinfeng Zhai Saishuai Li Xiaojuan Jia Jiaqiang Chen Qi Wang Yan Pi Zhuojun Ma Zixia Zhao Keji Jiang

Hypoxia represents a pervasive selective pressure in aquaculture systems, prompting aquatic organisms to develop distinct tolerance strategies through diverse physiological and biochemical responses. The common carp (Cyprinus carpio), a species characterized by extensive geographical distribution and a long history of artificial selection, exhibits considerable inter-varietal and inter-population variation in hypoxia tolerance. Nevertheless, the mechanistic basis underlying hypoxia tolerance in the context of domestication remains poorly understood. The present study employed mirror carp (C. carpio var. specularis), a highly domesticated strain with proven hypoxia tolerance, and Hebao red carp (C. carpio var. wuyuanesis), a locally distributed, minimally domesticated variety that is relatively sensitive to hypoxia, to investigate the metabolic responses and underlying mechanisms associated with hypoxia tolerance. Focusing on muscle and liver tissues, we performed separate statistical and bioinformatics analyses of the metabolic profiles derived from the two strains. The results revealed that hypoxia exposure induced only minor perturbations in energy metabolism in mirror carp, whereas Hebao red carp exhibited a profound metabolic depression in muscle, accompanied by signs of insufficient energy production in the liver. Notably, an enhanced nitric oxide (NO) pathway, implicated in vascular tone regulation and oxygen delivery, was observed in the liver of mirror carp but not in that of Hebao red carp. Collectively, these findings delineate distinct metabolic patterns between common carp strains subjected to differing degrees of domestication, which may account for their differential hypoxia tolerance. Moreover, this study offers a theoretical foundation for the selective breeding of hypoxia-resilient fish strains in aquaculture practices.

Fishes doi: 10.3390/fishes11090535

Authors: Feng-You Lin Yu-Chen Wu Agus Triawan Chin-I Chang Chih-Yu Lo Hong-Thih Lai

This study compared the survival and growth of four wild-caught mud crab species (Scylla serrata, S. paramamosain, S. tranquebarica, and S. olivacea) under controlled conditions. The experiment was divided into two stages: Stage I (crablet to juvenile) and Stage II (juvenile to adult). At the end of each stage, the sex ratio, survival rate (SR), body weight (BW), carapace width (CW), weight gain (WG), and average daily gain (ADG) were calculated. The results showed that S. tranquebarica had the highest cumulative survival (67.6%), whereas S. serrata recorded the lowest (38.6%). Growth performance varied among species and between sexes. Male S. serrata demonstrated the highest growth potential with a final CW (11.77 cm), BW (447.1 g), WG (428.61 g), and ADG (3.93 g/day). Conversely, S. olivacea exhibited the lowest overall growth performance in Stage II. Males of S. serrata and S. paramamosain showed superior final growth performance over females. Furthermore, S. tranquebarica showed phase-dependent growth acceleration, transitioning from the lowest growth in Stage I to the second highest in Stage II. Further studies are needed to evaluate S. tranquebarica as a potential alternative or complementary culture species to S. serrata.

Fishes doi: 10.3390/fishes11090534

Authors: Dongxu Yang Xirui Xu Shengmao Zhang Zuli Wu Tianfei Cheng Jianglong Que Siyao Wu Fei Wang

Morphometric information provides quantitative descriptors of cetacean size and shape and may support future assessments of individual condition and population status when combined with appropriate biological calibration. However, conventional contact-based measurements are difficult to apply to free-ranging Yangtze finless porpoises (Neophocaena asiaeorientalis). UAV imagery offers a non-contact means of acquiring porpoise morphometric data, but automated workflows for converting UAV observations into reliable body-surface measurements remain limited. To address this gap, an oriented detection-guided SAM2 morphometric workflow, termed ODG-SAM2-Morph, was developed to automatically extract body-surface morphometric parameters from UAV imagery. The workflow integrates YOLO26-OBB for oriented target localization, SAM2 for prompt-guided body-surface segmentation, and differentiated morphometric extraction strategies for complete-body and partial-body samples. Guided by oriented detections, the small SAM2 model with the R-Box + 1FG prompt generated body-surface masks with mean IoU, mean Dice, Precision, and Recall values of 0.824, 0.901, 0.883, and 0.932, respectively. For complete-body samples, automatically extracted body-length and body-width parameters showed preliminary agreement with manual measurements. For 114 partial-body samples, the automatically extracted maximum visible body width agreed reasonably well with manual measurements, with a MAE of 3.32 cm and a MAPE of 11.93%. Continuous-sequence analysis further showed that the representativeness of maximum visible body width depended on trunk exposure, contour clarity, body posture, and inter-frame stability. By converting UAV observations into quantitative image-derived morphometric measurements, ODG-SAM2-Morph provides a practical basis for non-contact morphometric monitoring of Yangtze finless porpoises under natural survey conditions.

Fishes doi: 10.3390/fishes11090531

Authors: Anton Lamboj Stephan Koblmüller

Cichlid fishes of the genus Rubricatochromis are widely distributed across western, central, and northern Africa, yet their taxonomy has long remained unstable because of overlapping morphological characters, variable coloration, and inconsistent use of species names. We present an integrative taxonomic revision of the genus based on mitochondrial DNA sequence data, molecular species delimitation analyses, morphometric and meristic analyses, qualitative assessment of live coloration, and a previously published multilocus phylogeny. Phylogenetic analyses recovered several deeply divergent lineages, some of which had already been informally recognized in the aquarium trade. Although morphological overlap among species was substantial, several taxa could be diagnosed by combinations of morphometric traits and coloration patterns. We describe four new species, Rubricatochromis gabonensis sp. nov., R. jebeli sp. nov., R. stephenthorntoni sp. nov., and R. vanheusdeni sp. nov.; validate R. fugax; and synonymize R. exsul, R. letourneuxi, R. paynei, and R. saharae with R. guttatus, as well as R. lifalili with R. stellifer. Several newly recognized taxa appear to have highly restricted distributions and may qualify as threatened, emphasizing the conservation importance of West and Central African river systems and the urgent need for biodiversity assessments and habitat protection in these understudied regions.

Fishes doi: 10.3390/fishes11090532

Authors: Xinxin Li Xiaoxiao Li Shuyuan Luo Fengzhuo Zeng Changpeng Yan Dong Huang

This study examined the effects of dietary carbohydrate levels on growth performance, immune response, and antioxidant capacity of male giant freshwater prawn Macrobrachium rosenbergii. Prawns with an initial body weight of 15.04 ± 0.08 g were fed for 9 weeks on five isonitrogenous, isolipidic diets formulated to contain 10%, 15%, 20%, 25%, and 30% carbohydrate (designated CHO10–CHO30). Weight gain rate and specific growth rate rose from CHO10 to CHO20 and then declined (peak in CHO20); broken-line regression of weight gain rate estimated the optimal dietary carbohydrate level at approximately 19.36% under the present experimental conditions. Moderate carbohydrate inclusion (15–20%) enhanced hepatopancreatic total antioxidant capacity (T-AOC), superoxide dismutase (SOD) and catalase (CAT) activities together with the transcription of cu/znsod, cat and glutathione peroxidase (gsh-px), whereas levels ≥ 25% lowered these defenses and raised hepatopancreatic malondialdehyde (MDA). High-carbohydrate diets also increased hemolymph glucose, triglyceride, total cholesterol and low-density lipoprotein cholesterol, progressively altered the mRNA expression of genes involved in the Toll-like receptor (TLR)/myeloid differentiation primary response 88 (MyD88) signaling pathway (upregulated tlr, myd88, relish and tumor necrosis factor; downregulated inhibitor of NF-κB alpha (IκB-α)), and altered the expression of apoptosis-related genes (downregulated B-cell lymphoma 2 (bcl-2), upregulated caspase-3). These results suggest that M. rosenbergii has an estimated optimal dietary carbohydrate level of approximately 19.36% under the present experimental conditions; intakes at or above 25% are associated with compromised hepatopancreatic health and growth, likely through the induction of oxidative stress, altered transcription of TLR/MyD88 pathway-related genes, and changes in apoptosis-related gene expression.

Fishes doi: 10.3390/fishes11090530

Authors: Miguel Torres-Rodríguez Ismael Hachero-Cruzado Jose Ignacio Navas-Triano

Substrate availability is a key environmental factor for burrowing bivalves, yet its physiological importance in adult clams remains poorly understood. This study evaluated the effects of short-term substrate manipulation on growth performance, intermediary metabolism, and fatty acid (FA) composition of adult Ruditapes decussatus. Clams were reared for 15 months either with or without sediment and subsequently exposed for 40 days to the opposite substrate condition. Growth performance, metabolic parameters (glucose, glycogen, lactate, triglycerides, and cholesterol), and tissue FA composition were determined. No mortality was recorded, and substrate manipulation had no relevant effects on growth performance. In contrast, substrate removal induced significant decreases in glucose, triglyceride, and cholesterol concentrations, together with increased lactate levels, while glycogen remained unchanged. Conversely, substrate addition did not modify metabolic parameters but promoted selective tissue FA remodeling, characterized by reduced saturated FAs and increased unsaturated, particularly long-chain polyunsaturated FAs. These findings demonstrate that adult R. decussatus exhibits considerable physiological plasticity, with metabolic and membrane lipid responses differing according to the type of substrate manipulation and the previous acclimation history. The results also highlight the value of integrating metabolic and lipid biomarkers with conventional growth indicators to improve the assessment of the physiological status of cultured clams.

Fishes doi: 10.3390/fishes11090529

Authors: Roselida Akinyi Opere Giulia Pascon Gloriana Cardinaletti Francesca Tulli

Lauric acid (LA), a medium-chain fatty acid abundant in coconut oil and Hermetia illucens larvae, has been reported to promote growth performance and exhibit antimicrobial and immunostimulatory properties. This review examines current studies on its effects on growth performance, intestinal health, microbiota modulation, and immune responses in aquatic species. Studies in finfish and crustaceans were evaluated according to the LA source, distinguishing purified LA, LA derivatives such as monoglycerides, and LA rich ingredients, when considering LA rich ingredients. Overall, LA was associated with changes in growth performance, feed efficiency, survival, intestinal morphology, gut microbiota, and immune and antioxidant responses, although effects varied with source, dose, species, and experimental conditions. Reported effects include increased villus height and goblet cell density, modulation of gut microbiota, altered cytokine expression, increased antioxidant enzyme activity, and reduced lipid peroxidation. Overall, LA appears to be a promising functional component in aquafeeds for finfish and crustacean species. Nevertheless, inconsistent experimental designs, differences in LA sources, and species-specific responses make direct comparisons among studies difficult. Further studies that use standardized experimental protocols, including consistent LA sources, dietary inclusion levels, trial durations and evaluation criteria, are needed to define optimal inclusion levels in different aquatic species.

Fishes doi: 10.3390/fishes11090528

Authors: Valeria Moncayo Fernando Sánchez-Orellana Leiner Maxi Gabriela Echevarría

Trace element contamination in Amazonian freshwater ecosystems threatens riverine food security. This study evaluated two post-harvest treatments—ethylenediaminetetraacetic acid (EDTA) and Lactobacillus fermentum—to assess cadmium (Cd) and lead (Pb) variations in edible muscle of four Amazonian fish species (Cichla monoculus, Pimelodus jivaro, Platynematichthys notatus, and Serrasalmus rhombeus). Concentrations were determined using ICP-OES. Platynematichthys notatus exhibited the highest baseline bioaccumulation, whereas C. monoculus showed the lowest. Although main treatment effects should be considered exploratory, distinct species-dependent trends emerged. EDTA achieved the highest Cd reduction in P. notatus (49.78%), while L. fermentum demonstrated notable Cd and Pb reductions in C. monoculus, P. notatus, and S. rhombeus. Conversely, relative concentration increases occurred in P. jivaro under both treatments, reflecting matrix-related effects. These findings suggest that post-harvest efficiency depends on fish species and metal type. Probiotic post-harvest processing represents a promising strategy for reducing dietary exposure to Cd and Pb in Amazonian fisheries, though optimizing operational parameters for community-level applications remains necessary.

Fishes doi: 10.3390/fishes11090527

Authors: Soko Nuswantoro Ming-Chang Hong Tsung-Meng Wu Guan-Jie Wang Bonien Chen Tzu-Yuan Sung

Red coloring determines the commercial value of blood parrot cichlids (Vieja melanurus × Amphilophus citrinellus). While synthetic astaxanthin (SA) is commonly used to improve hue, its expensive cost has prompted the quest for more sustainable alternatives. This 60-day study looked at shrimp waste extract (SWE) as a dietary supplement for color improvement. Fish were assigned to five diets: basal control (G1, 0 mg/kg SA: 0 mg/kg SWE), SWE alone (G2, 0 mg/kg SA: 7.7 mg/kg SWE), high SA (G3, 90 mg/kg SA: 0 mg/kg SWE), moderate SA (G4, 45 mg/kg SA: 0 mg/kg SWE), and mixed SA with SWE (G5, 45 mg/kg SA: 7.7 mg/kg SWE). Growth and CIELAB skin pigmentation were evaluated. Growth performance was consistent across all treatments. Colorimetric study found that while the SWE alone (G2) significantly improved pigmentation compared to the control, it was less effective than the high-SA diet. However, incorporating SWE into the moderate-SA diet (G5) resulted in a promising complementary response. Despite having half the SA concentration, G5 achieved pigmentation that was comparable or superior to the G3 diet by the end of the feeding trial. These data revealed that, while SWE has lower independent activity, it is an effective complementary additive for shortening the feeding period required to achieve a similar redness. Finally, SWE enables the partial substitution of synthetic astaxanthin, providing a cost-effective and environmentally sustainable nutritional strategy for the ornamental aquaculture business.

Fishes doi: 10.3390/fishes11090526

Authors: Hannah Malene Jensen Kaan Kumas Per Walter Kania Kurt Buchmann Eleni Ntokou Nana Wentzel Thorringer

We here report immunomodulatory effects of feeding with microbial single-cell protein (SCP from Methylococcus capsulatus) on female rainbow trout (Oncorhynchus mykiss) following replacement of conventional feed proteins in a 30-day feeding period. Conventional protein ingredients (soy protein concentrate, fishmeal (FM), wheat gluten meal and corn gluten meal) were partially replaced with microbial SCP at graded inclusion levels (0, 4, 6 and 8% SCP). Growth performance parameters, such as final body weight (FBW) and final fish length (FL), were elevated at 6% SCP inclusion. In the present investigation we found that immune gene expression in the liver and spleen was regulated following feeding microbial SCP in a concentration-dependent way. Feed with 4% SCP inclusion induced a significant upregulation of the hepatic expression of IL-10 (p < 0.05), whereas splenic expression of IL-6 and Cathelicidin-2 genes were downregulated. No significant differences were observed at 6% SCP inclusion. At 8% SCP inclusion, splenic expression of multiple immune-related genes, including those encoding Cathelicidin-2, CD8, IgM, IL-6, and SAA, was significantly downregulated, along with hepatic expression of Cathelicidin-1 (p < 0.05). Although immune gene expression was downregulated at 8% SCP inclusion, growth performance was not adversely affected. These findings indicate that up to 8% of conventional feed protein can be replaced with microbial SCP without compromising growth performance, although immune gene regulation varies depending on tissue and inclusion level. Gene regulation and health effects induced by feeding rainbow trout with high microbial SCP inclusion feed and over longer time periods should be further investigated. For this purpose, we recommend studies on functional immune parameters such as vaccine responsiveness and antibody production.

Fishes doi: 10.3390/fishes11090525

Authors: Leiming Yin Hongyang Chen Shuang Song Zihang Wang Hexiang Yang Jianyu Sun Shengkai Lin Binbin Xing Qingxia Li Tao Tian

Xiangyun Bay Marine Ranch, in the Bohai Sea, China, is an important fishery resource area but has long been affected by eutrophication, habitat destruction, and overfishing. To support resource conservation and management, this study combined environmental DNA (eDNA) metabarcoding, acoustic survey, and a traditional net survey to assess fish resources. The traditional net survey collected 18 fish species (2143 individuals), with Speartailed goby (Chaeturichthys stigmatias) and Indian flathead (Platycephalus indicus) as the dominant species (~70% of total). An acoustic survey revealed that fish resource density in the reef area ranged from 6.05 × 10−5 to 9.38 × 10−5 ind/m2, with vertical distribution concentrated in the 1–3 m water layer; strong scatterers (−47 to −42 dB) at 3 m depth indicated benthic large individuals. The eDNA analysis generated 1,091,731 high-quality sequences assigned to 39 fish species, with dominant species including Kammal thryssa (Thryssa kammalensis), Yellow-spotted slipmouth (Nuchequula flavaxilla), and Large-mouth naked goby (Gymnoglobus macrognathos). In conclusion, the acoustic survey demonstrates unique advantages in assessing spatial distribution of fishery resources, while eDNA technology serves as an effective supplement to traditional net surveys. Their combined application provides more accurate scientific evidence for the production management and sustainable utilization of marine ranches.

Fishes doi: 10.3390/fishes11090524

Authors: Zhou Zhou Zhengxi Wei Xinle Zhang Xianbao Cheng Junlin Deng Xin Han Ning Wu

Reliable identification and behavioural tracking of individual fish are increasingly required in aquaculture monitoring and ecological conservation, yet such tasks often rely on extremely limited image samples. Individual-level fish recognition remains challenging because subtle inter-individual variations in stripe patterns, spots and body markings are difficult to distinguish, while annotated datasets are scarce and costly to construct. To address these challenges, this study proposes Squeeze-and-Excitation Feature-Fusion Window Transformer (SEFFwin), a lightweight vision Transformer derived from Swin Transformer V2 for ultra-fine-grained fish recognition under extreme few-shot conditions. Through structured pruning, the SEFFwin backbone contains approximately 11.30 million parameters, excluding the task-specific classification layer. To support evaluation, we construct Koi-fish-3, a dedicated few-shot benchmark consisting of three individual koi categories, with only two training images and 100 validation images per class. Transfer learning, data augmentation and knowledge distillation are further incorporated to improve model optimisation under severely limited supervision. Experimental results show that SEFFwin achieves 92.0% top-1 accuracy on Koi-fish-3, outperforming representative lightweight baselines while maintaining high computational efficiency. Post-hoc interpretability analysis indicates that SEFFwin consistently attends to biologically meaningful stripe and spot patterns and can weakly localise class-specific regions. These findings demonstrate that SEFFwin provides an accurate and efficient solution for individual fish recognition under extreme data scarcity, offering practical value for intelligent aquaculture and ecological monitoring, while also providing insights into compact Transformer design for low-resource fine-grained recognition.

Fishes doi: 10.3390/fishes11090523

Authors: Alaa M. Younis Khaled Y. AbouelFadl Khaled Mohammed-Geba Doaa Hamed-Mohamed Mostafa A. Khaled

Global inland fisheries depend on large reservoirs, yet many assessments assume spatial homogeneity despite complex embayed morphometry. We tested whether khor-scale structure within Lake Nasser, Egypt, explains variation in two commercially important catfishes. Six distinct khors spanning the north–south axis (Ghazal, Sheniara, Garf Hussein, Amada, Toshka, and Hamedo) were sampled with standardized effort (72 net-nights; 12 per khor, 3 representative areas ≥ 500 m apart × 4 campaigns, March–June 2021), yielding 398 fish (268 Chrysichthysauratus, 130 C. rueppelli). Abundance was expressed as standardized CPUE (fish·net-night−1). C. auratus CPUE ranged from 2.83 (Ghazal) to 5.92 (Garf Hussein), while C. rueppelli CPUE was relatively uniform (1.50–1.92). C. auratus attained the largest TL in Ghazal (25.51 ± 2.9 cm) and the highest condition K in Garf Hussein (1.46 ± 0.18). C. rueppelli attained the greatest TL and weight in southern khors, especially Hamedo (23.3 ± 2.33 cm, 146.7 ± 30.5 g), while its highest condition was in Toshka (1.30 ± 0.15). Sex ratio was significantly female-biased for C. auratus (92 M:176 F, 1:1.91, p < 0.001) but not for C. rueppelli (55 M:75 F, 1:1.36, p = 0.079). Results show embayment-scale CPUE and condition, not whole-lake means, capture key population patterns, improving precision of mega-reservoir fisheries management.

Fishes doi: 10.3390/fishes11090522

Authors: Yali Wang Haipeng Cao

The rapid intensification of global aquaculture, particularly the widespread application of recirculating aquaculture systems (RAS), has substantially improved aquatic product yield [...]

Fishes doi: 10.3390/fishes11090521

Authors: Jong Ryeol Choe Junseong Park Ju-Ae Hwang Hyeongsu Kim

This study compared conventional aquaponics (AP), biofloc-based aquaponics (FLOCponics, FP), and hydroponics (HP) in terms of juvenile eel (Anguilla japonica) growth, ‘Caipira’ lettuce (Lactuca sativa) productivity, and water-quality characteristics. The AP and FP treatments each comprised three replicate fish tank–plant cultivation systems stocked with 119 eels per tank, whereas HP was included as a control for plant production. Eels reared in FP exhibited a higher estimated final biomass and specific growth rate and a lower feed conversion ratio than those reared in AP. The total and shoot biomass of lettuce were higher in FP than in AP and were comparable to those obtained in HP.

Fishes doi: 10.3390/fishes11090520

Authors: Piotr Traczuk Tomasz Kajetan Czarkowski Andrzej Kapusta

Catch-and-release (C&R) fishing has become a common practice. Anatomical hooking location (AHL) can be crucial to fish survival. The length of the slack line connecting the hook to the rest of the rig (leader) can affect both the anatomical hooking location and catch efficiency. In this study, we set out to determine whether such a scenario would occur. A total of 2826 fish representing nine species were captured during the study. The shorter leader (15 cm) yielded 1462 fish (51.7%), whereas 1364 fish (48.3%) were captured using the 40 cm leader. Mean catch per unit effort (CPUE) was higher for the shorter leader (44.3 fish h−1) than for the longer leader (41.3 fish h−1). Fish were most frequently hooked in superficial, non-critical anatomical hooking locations within the mouth (upper and lower jaw and mouth corners). Safe hook placements accounted for 88.0% of captures with the 15 cm leader and 78.7% with the 40 cm leader. The research supported our hypothesis and predictions: a shorter leader is safer for fish and less likely to cause deep hooking in critical anatomical locations. On the other hand, shallower hooking was associated with higher catch efficiency. Our findings can help anglers design terminal tackle appropriately.

Fishes doi: 10.3390/fishes11090519

Authors: Shouguo Yang Donghui Zhang Hebert Ely Vasquez Fen Cheng Xiangyu Wu Luqing Pan Xianming Tang

This study investigated the effects of glycerol monolaurate (GML) on the growth performance, physiological efficacy, intestinal structure, and microbiota of hybrid juvenile ♀ Epinephelus fuscoguttatus × ♂ E. lanceolatus. A total of 594 groupers were administered diets supplemented with 0, 2, 4, 6, 8, or 10 g/kg of GML over an 80-day period. The findings indicated that the group receiving 4 g/kg GML supplementation demonstrated significantly enhanced growth performance, as evidenced by increased weight gain, specific growth rate, and a reduced feed conversion ratio compared with the control and other experimental groups. This growth enhancement was associated with elevated catalase and glutathione levels, suggesting improved antioxidant capacity that may contribute to enhanced immune function. Furthermore, fish in the 4 g/kg group exhibited increased digestive enzyme activity and significantly improved intestinal morphology, characterized by thicker muscular layers and a greater fold width and height. Furthermore, compared with the control group, GML supplementation elevated the relative abundance of Proteobacteria while reducing that of Firmicutes at the phylum level. At the genus level, GML markedly suppressed the relative abundance of Mycoplasma and Vibrio. These compositional alterations are potentially linked to improved energy acquisition and a decreased risk of pathogenic infections. Collectively, these results reveal that GML acts as a promising functional feed additive to boost growth performance, optimize digestive capacity, and sustain intestinal structural integrity in hybrid grouper. Based on these results, the optimal GML supplementation dose was determined to be 4 g/kg, providing valuable insights into the role of GML in aquaculture practices for hybrid grouper.

Fishes doi: 10.3390/fishes11090518

Authors: Melissa Herrera-Perez Débora Machado Fracalossi Virginia Fonseca Pedrosa Renata Oselame Nobrega José Maria Monserrat Luis Alberto Romano Ronaldo Olivera Cavalli

The yellow clam, Amarilladesma mactroides, is an abundant component of the intertidal infauna of the southwestern Atlantic Ocean and an important source of food and income for local communities. In recent years, this species has been increasingly affected by anthropogenic and environmental pressures, contributing to the decline and collapse of several populations. In this study, we characterized the reproductive cycle of A. mactroides in the southernmost region of Brazil using standard approaches, including gonadal histology and biometric parameters, complemented by analyses of proximal composition and fatty acid profiles. Monthly samples of ≥100 clams were collected from October 2021 to September 2022. The results revealed two distinct reproductive peaks: a major peak from October to December (austral spring–summer) and a less pronounced peak from May to July (autumn–winter). Although gonadal histology, particularly oocyte diameter, provided the primary evidence for defining these reproductive peaks, the condition index and concentrations of total lipids and n-3 polyunsaturated fatty acids (n-3 PUFA) also proved useful indicators of reproductive activity. These findings provide new insights into the reproductive dynamics of A. mactroides in southern Brazil and may contribute to the development of strategies for the sustainable management, conservation and aquaculture of this ecologically and socioeconomically important bivalve.

Fishes doi: 10.3390/fishes11090517

Authors: Luis Alarcón-Martínez Miguel Guzmán-Yance César Montes-Petro Carlos Tapia-Pacheco Diana Madariaga-Mendoza José Espinosa-Araujo Víctor Atencio-García

The development of first-feeding protocols is a critical step in the domestication of native fish species for aquaculture. This study aimed to evaluate the first-feeding management of Pseudopimelodus atricaudus, a Neotropical catfish with aquaculture potential, using four prey types: Artemia nauplii (AN), decapsulated Artemia cysts (DC), wild zooplankton smaller than 400 µm (WZ < 400), and larger than 400 µm (WZ > 400). Larvae of P. atricaudus begin exogenous feeding at 30 h post-hatch (1.5 ± 0.02 mg and 5.2 ± 0.01 mm) and have a maximum mouth width of 611.4 ± 11.7 µm. Larvae fed WZ > 400 µm showed significantly higher growth (13.7 ± 0.2 mm, 94.6 ± 1.8 mg) and final survival (91.2 ± 2.2%) compared to the other treatments (p < 0.05), as well as a greater intestinal fold height (129.8 ± 8.4 µm, p < 0.05). No significant differences in hypoxia stress resistance were detected among treatments (p > 0.05). This study demonstrated that WZ > 400 µm is an appropriate prey for managing the first feeding of P. atricaudus.

Fishes doi: 10.3390/fishes11090516

Authors: Letícia Almeida Barbosa Gomes Thiago Machado da Silva Acioly Lucas de Oliveira Vieira Felipe Polivanov Ottoni Marcelo Francisco da Silva Diego Carvalho Viana

This study investigates the length–weight relationship, growth patterns, and population structure of Prochilodus nigricans in a tropical river environment, providing biometric information relevant to ecological studies, fisheries assessment, and conservation planning. A total of 139 individuals were sampled across rainy and dry seasons, and biometric variables (BD—Body Depth, TL—Total Length, SL—Standard Length, TW—Total Weight, and GW—Gonad Weight) were compared using descriptive statistics and regression analyses. Significant differences in biometric parameters were observed between seasons and sexes. Among the sampled individuals, body depth, standard length, total length, and total weight were significantly higher during the rainy season for both sexes; however, these differences should be interpreted with caution because different gill-net mesh sizes were used between hydrological periods. Gonad weight and gonadosomatic index (GSI) differed significantly between males and females in both seasons. A significant overall effect of season was detected for gonad weight, although pairwise seasonal differences were observed only in males, whereas no significant seasonal effect was detected for GSI. Length–weight relationships indicated isometric growth in both sexes. These results provide baseline biometric information useful for future ecological studies and complementary fisheries assessments of P. nigricans in the Tocantins–Araguaia Basin.

Fishes doi: 10.3390/fishes11090515

Authors: Haopeng Hu Yan Liu Longyu Liu Peng Gao Yanming Sui Shuai Han Mei Jiang Lei Li

Understanding niche differentiation and interspecific coexistence patterns of macrobenthos provides critical references for ecological assessment of bivalve aquaculture. Seasonal field surveys (Autumn 2023–Summer 2024) across 12 sampling sites were conducted in an intensive Meretrix meretrix tidal flat farm in Rudong, Jiangsu. Synchronous water depth, sediment grain size and total organic carbon (TOC), and salinity were measured at each station to characterize habitat gradients; no unfarmed reference tidal flats were included, so all community patterns only reflect within-farm variation. The study area has sustained 10-year continuous bottom culture with baseline juvenile stocking density of 250 ind./m2 and twice-yearly manual harvesting. A total of 58 macrobenthic taxa were identified, and 13 dominant species were screened with a dominance index threshold Y > 0.02. All abundance data were fourth-root-transformed before Bray–Curtis community analysis to reduce bias of hyper-abundant taxa. Standardized Shannon niche breadth (0–1 normalized, r = 48 site–season composite units) and permutation-tested (999 replicates) Pianka niche overlap/similarity coefficients were calculated to quantify resource utilization similarity. Niche breadth ranged from 0.018 to 0.971, with farmed M. meretrix showing the maximum value, indicating broader seasonal resource adaptation. High niche overlap (>0.50) was detected between M. meretrix and four wild dominant species (Nephtys californiensis, Moerella iridescens, Lingula anatina, Umbonium thomasi). Notably, niche metrics derived solely from spatial abundance data cannot directly confirm interspecific competition or trophic segregation; the stable coexistence observed in our assemblage is tentatively hypothesized to be driven by vertical sediment partitioning and divergent feeding guilds based on published functional studies, without direct in situ trophic or stratified sediment evidence from this work. Hierarchical UPGMA clustering (0.35 Bray–Curtis distance threshold) and corrected NMDS ordination (48 site–season units, dominant-species fitted vectors) illustrated distinct functional groups. Based on the observed niche convergence among filter-feeding bivalves under local farming conditions, the range of 230–280 ind./m2 is presented as an observational reference. Controlled manipulative experiments with gradient stocking densities are needed to test whether this range can balance aquaculture yield and benthic biodiversity.

Fishes doi: 10.3390/fishes11090514

Authors: Mark-Anthony Falzon Patrick J. Schembri

An association of Blue runner, Caranx crysos (Carangidae), with two species of rays, Common stingray Dasyatis pastinaca (Dasyatidae) and Bull ray Aetomylaeus bovinus (Myliobatidae), in which an individual C. crysos (the follower fish) follows a foraging ray (the nuclear species), is described, based on a sample of 61 video clips. Follower fish show three types of behaviour: swimming under the pectoral fin of the nuclear ray, swimming above the mid-dorsal line of the nuclear ray and very close to it, or swimming above the ray and darting from side to side. The first two of these behaviours seem to be species-specific as the first is only shown when the nuclear ray is A. bovinus and the second when the nuclear ray is D. pastinaca. Following fish do not allow conspecifics to approach the nuclear ray but are mostly indifferent to non-conspecifics doing so. The following fish benefit from the association by feeding on prey disturbed by the foraging activities of the nuclear ray but the nuclear ray is unreactive to the following fish, suggesting that this is a case of trophic commensalism.

Fishes doi: 10.3390/fishes11090513

Authors: Ahmed E. Elshafey Shuchang Cao Sebastianus Ken Chandra Bin Wen Zaizhong Chen

Cold stress disrupts redox homeostasis and skin structural integrity in ornamental koi carp (Cyprinus carpio). To address the unclear long-term effects of astaxanthin (AX), this study examined 90-day dietary supplementation on growth and skin-derived antioxidant mechanisms during cold shock and recovery. Koi carp were administered with one of the 5 diets containing the following 0 mg/kg (AX0), 25 mg/kg (AX25), 50 mg/kg (AX50), 75 mg/kg (AX75) and 100 mg/kg (AX100) of astaxanthin for 90 days then growth performance are measured; antioxidant of the fish skin was assessed thereafter they were exposed to an acute transfer to a temperature of 13 °C; MDA, GSH, SOD, CAT, protein carbonyls, and GPX were measured in skin samples collected after 90 days of dietary AX, following cold-stress exposure, and after the recovery period. Transcriptomic analysis and protein–protein association network analysis were performed for the AX0 and AX75 groups following cold-stress exposure and after the recovery period. AX75 treatment showed the highest growth performance. Under cold-stress conditions, the AX0 group exhibited higher MDA levels and lower SOD activity, whereas the AX75 group showed lower MDA levels and higher SOD activity. During the recovery period, AX75 showed increased CAT activity and GSH levels, along with low levels of MDA and protein carbonyls in comparison to the AX0 group. Transcriptomic analysis revealed diet-associated differential expression of candidate genes related to pentose phosphate and redox metabolism. Overall, the results of this study showed that 75 mg/kg astaxanthin enhanced growth and produced the strongest antioxidant response against cold stress and assisted in recovery.

Fishes doi: 10.3390/fishes11090512

Authors: Sevasti-Aliki Kounida Michail-Aggelos Valsamidis Sofia Pappou Vasileios Bakopoulos

European seabass (Dicentrarchus labrax) hematology is widely used in nutrition, welfare, stress and health studies, yet results from different laboratories are often difficult to compare. This critical narrative review examines how preanalytical handling, analytical procedure and biological context affect that comparability. It is written for researchers, diagnostic laboratories and aquaculture health teams that collect or use D. labrax blood data. Primary European seabass studies are discussed directly where they provide quantitative operating conditions, method comparisons or measurable biological changes. Manual microscopy, automated analyzers and flow cytometry are considered separately because nucleated erythrocytes and thrombocytes create different sources of error in each approach. The review distinguishes practical quality-control checks from the fuller reporting required for reproducibility and separates published operating conditions from numerical limits that have not been validated for the species. Seasonal studies show large coordinated shifts in red blood cell count (RBC), hemoglobin concentration (Hb) and hematocrit (Hct), whereas white blood cell count (WBC) and thrombocyte results remain particularly dependent on cell definition and analytical method. Published pooled estimates are useful for broad comparison but not as universal diagnostic limits. The most defensible use of European seabass hematology is therefore within a defined population, a stated sampling protocol and a method whose performance is known for the intended measurement.

Fishes doi: 10.3390/fishes11090511

Authors: Hee-Jung Lee Jong-Won Park Jeong-Ho Lee Kwang-Sik Choi Hyun-Ki Hong

This study investigated seasonal variation in tissue growth, reproductive status, energy reserves, and digestive tubule condition in the Pacific oyster, Magallana gigas, cultured in an off-bottom intertidal rack system in Garorim Bay on the west coast of Korea. Monthly samples of adult oysters were collected from February 2009 to December 2010. Condition index (CI), total carbohydrate content, reproductive stage, female reproductive effort estimated by indirect enzyme-linked immunosorbent assay (ELISA), and digestive tubule atrophy (DTA) were measured concurrently in individual oysters. Gametogenesis was largely synchronized between sexes and was strongly associated with seasonal sea surface temperature (r=0.84, p<0.0001). Carbohydrate content peaked in early spring and declined during the spawning season. In females, carbohydrate content was negatively correlated with gonad somatic index (GSI) (r=−0.30, p<0.0001), suggesting that oysters investing more heavily in egg production tended to have lower remaining carbohydrate reserves. GSI showed interannual variation in spawning timing, peaking at 37.9% in June 2009 and 37.0% in July 2010. DTA showed temporal variation, with relatively elevated values in late summer–early autumn 2009 and mid-winter 2010. The late-summer 2009 increase in DTA coincided with a marked decline in salinity; however, monthly mean analyses did not establish a causal relationship between salinity and DTA. Together, these results indicate that the seasonal physiological condition of intertidal rack-cultured oysters reflects a dynamic balance between reproductive investment, carbohydrate reserves, and digestive gland condition, with this balance potentially modified by seasonal environmental variability. These results provide a cross-sectional, multi-parameter baseline for seasonal monitoring of reproductive status, energy reserves, and digestive tubule condition in intertidal rack-cultured oysters in Garorim Bay.

Fishes doi: 10.3390/fishes11090510

Authors: Shujie Wan Jing Cheng Zhijun Wang Guodong Li

High-frequency broadband acoustics can provide fine spatial resolution for near-range fish measurements, but the performance and limitations of beam-position-resolved backscatter measurements require careful evaluation. This proof-of-concept study examined one commercially sourced, dead, previously frozen specimen of each of three cultured fishes: golden pompano (Trachinotus ovatus; 24.4 cm), mandarin fish (Siniperca chuatsi; 29.1 cm), and large yellow croaker (Larimichthys crocea; 31.2 cm). A 650–750 kHz narrow-beam system was referenced to a 10.3 mm tungsten-carbide sphere, and matched-filter pulse compression and 1° stepwise scanning were used to estimate a beam-position-resolved backscatter metric along each body. At broadside incidence, the section-summed backscatter indices were −33.61, −22.45, and −33.07 dB for the T. ovatus, S. chuatsi, and L. crocea specimens, respectively. The section-summed abdominal backscatter index, in the region occupied by the swimbladder in the post-thaw X-ray images, exceeded the arithmetic mean of the head and tail group indices by 9.71 ± 1.84 dB (range: 8.27–11.86 dB). Tailward beam positions fell below the noise floor at approximately 12.5% of the expected scan positions for S. chuatsi and 22.2% for L. crocea. A 15° departure from broadside reduced the section-summed index by 3.73–11.43 dB. Kirchhoff-ray-mode (KRM) simulations based on post-thaw dual-view X-ray geometry were broadly consistent with the specimen-level contrast observed among the preserved specimens, but were 0.92–2.74 dB lower than the corresponding broadside section-summed measurement indices at 700 kHz. These differences are not a quantitative validation because the measured and modeled estimators, frequency weighting, geometry, and tissue parameters were not equivalent. These results demonstrate the feasibility of a calibrated beam-position workflow for preserved specimens, while not establishing live-fish target strength, species benchmarks, or biomass-estimation performance.

Fishes doi: 10.3390/fishes11090509

Authors: Jinghua Fu Jianpeng Li Ke Zhang Minjun Xu

To evaluate the economic and ecological potential of black soldier fly larvae (BSFL) slurry as a fishmeal alternative, 270 juvenile Pangasius (initial body weight: 7.20 ± 0.07 g) were acclimated for two weeks and randomly allocated to three dietary treatments (T0, T1, T2), with three biological replicates per treatment. The feeding trial lasted six weeks (42 days). Fish in T0 were fed the basal diet, while T1 and T2 diets replaced 50% and 100% of fishmeal with BSFL on an isonitrogenous basis, respectively. At trial termination, whole-body proximate composition, muscle texture, and intestinal microbiota were analyzed. BSFL inclusion at 50–100% fishmeal replacement did not compromise growth performance. Moisture and ash content did not differ among treatments (p > 0.05), whereas BSFL supplementation significantly altered muscle texture, reducing hardness and resilience while increasing springiness, chewiness, cohesiveness, and adhesiveness. Both 50% and 100% BSFL replacement enhanced hepatic antioxidant capacity, evidenced by significantly higher superoxide dismutase (SOD) activity (p < 0.05). BSFL also modulated intestinal microbiota and enhanced community evenness, though without significant intergroup differences in bacterial abundance (p > 0.05). This study demonstrated that BSFL could replace 50–100% of fishmeal in diets for juvenile Pangasius, maintaining growth performance while modifying nutritional profiles, muscle texture, hepatic antioxidant status, and intestinal microbiota. Nevertheless, 100% fishmeal replacement triggered distinct shifts in intestinal microbial composition despite satisfactory growth, and the 50% substitution level was, therefore, recommended as a safe proportion for practical aquafeeds.

Fishes doi: 10.3390/fishes11090508

Authors: Vitória Pereira Sílvia F. S. Pires Pedro Bem-Haja Andreia C. M. Rodrigues Amadeu M. V. M. Soares Luís E. C. Conceição Mário Pacheco Rui J. M. Rocha

Conventional bivalve depuration protocols may compromise organoleptic and nutritional quality, largely as a consequence of fasting. This study investigates an innovative post-depuration feeding strategy in the clam Ruditapes decussatus using microencapsulated diets containing Nannochloropsis sp. supplemented with either a standard dose of vitamins C and E (MV) or a high dose—4× the standard level—of these vitamins (MV+). A three-phase experiment was conducted comprising 24 h of depuration, 2 h of post-depuration feeding, and 6 days of refrigerated storage at 5 ± 1 °C. Clams were sampled after feeding (PF) and after refrigerated storage (PS) and assessed for condition index (CI), vitamin C and E contents, antioxidant defense markers, including catalase activity (CAT) and total glutathione (tGSH), and oxidative damage, assessed through lipid peroxidation (LPO). CI did not differ significantly among dietary treatments. At PF, dietary treatment modulated antioxidant-related responses, particularly in the MV+ group. In the digestive gland, MV+ showed significantly lower LPO than the Control at PF, whereas after refrigerated storage this response was reversed. These findings indicate that the potential benefits associated with vitamin-enriched post-depuration feeding were not fully retained, with increased LPO at PS indicating greater oxidative damage. Further research is required to optimize this feeding strategy and evaluate its feasibility at commercial scale.

Fishes doi: 10.3390/fishes11090507

Authors: Sandra Edith Olmeda-de la Fuente Jorge Homero Rodríguez-Castro Jorge Alejandro Rodríguez-Olmeda Filiberto Toledano-Toledano Frida Carmina Caballero-Rico José Alberto Ramírez-de León Gonzalo Hernández Ibarra

Small-scale fisheries management is a critical challenge for global fisheries sustainability. This study diagnoses the institutional failures behind overexploitation and regulatory non-compliance in Mexico’s shark-cazón fishery (predominantly Rhizoprionodon terraenovae). Using the Institutional Analysis and Development (IAD) Framework and Ostrom’s Social-Ecological Systems (SES) approach, we assessed the catch series (1976–2014) and institutional robustness. Results show a 77% surplus over the Maximum Sustainable Yield (MSY), with an average catch of 51,417 tonnes per year against a biological limit of 29,040 tonnes. The diagnosis reveals undefined access limits, exclusively state-run monitoring, sanctions provided for in law but not applied participatorily, and the absence of local conflict-resolution mechanisms. These findings suggest that overexploitation is not an inevitable biological failure but the outcome of a command-and-control design that inhibits collective action and erodes rule legitimacy. This study contributes to the common-pool resource governance literature by extending Ostrom’s framework and Hønneland’s compliance model to a previously underrepresented Latin American elasmobranch context. Based on this diagnosis, we recommend transitioning toward polycentric governance—with nested community monitoring, effectively enforced graduated sanctions, and local conflict-resolution mechanisms—as a strategy for improving regulatory compliance in data-limited fisheries.

Fishes doi: 10.3390/fishes11090506

Authors: Barbara Zorica Danijela Šantić Ivana Lepen Pleić Marija Šestanović

Ichthyoplankton provide critical insight into spawning activity, recruitment potential, and environmental drivers shaping fish populations. Despite their ecological importance, broad-scale ichthyoplankton studies in the Adriatic Sea remain limited. We analysed ichthyoplankton assemblages across the eastern Adriatic Sea, precisely five study areas—west coast of Istrian peninsula (I), Kvarner and Kvarnerić (K), northern middle Dalmatia (Z), wider area of Jabuka Pit (J), and southern Dalmatia (D), during two consecutive summers (2019–2020), combining plankton sampling using WP2 with DNA barcoding to improve taxonomic resolution. A total of 1382 eggs and 407 larvae were identified, representing 20 families and 34 species. Pelagic taxa dominated the assemblage, with anchovy (Engraulidae) accounting for more than 80% of ichthyoplankton. Spatial patterns revealed consistently higher abundances in Kvarner and Kvarnerić, the wider Jabuka Pit area, and southern Dalmatia—regions characterized by enhanced productivity, retentive circulation, or upwelling. Alpha biodiversity indices indicated high interannual similarity, while ANOSIM and SIMPER analyses confirmed significant differences (p < 0.05) among regions, driven primarily by Engraulidae and secondarily by Bothidae, Pomacentridae, Scombridae, Serranidae, and Sparidae. Redundancy analysis showed that temperature and chlorophyll-a were key environmental drivers influencing both pelagic and coastal taxa. These findings provide essential baseline information on ichthyoplankton dynamics in the eastern Adriatic Sea and highlight key spawning and nursery areas relevant for fisheries management. This study also demonstrates the value of integrating DNA barcoding with ecological analyses to strengthen ichthyoplankton monitoring in a rapidly changing marine environment.

Fishes doi: 10.3390/fishes11090505

Authors: Yang Guo Mingguo Lu Weidong Xu Hao Liu Silei Xia Hongyan Tian Zhiqiang Xu Jianhua Ming Jing Chen Heyun Yang Bo Liu Hui Cao Wuxiao Zhang Aimin Wang

Astragalus membranaceus and Atractylodes macrocephala are traditional Chinese medicinal herbs known for their potential anti-inflammatory and immunomodulatory properties; however, their effects on the growth performance, muscle composition, and intestinal microbiota of aquatic animals remain poorly understood. A total of 480 healthy juvenile red swamp crayfish (Procambarus clarkii) with uniform size (initial mean body mass 5.24 ± 0.04 g) were randomly assigned to four isonitrogenous diets containing 0, 250, 500, and 750 parts per million (ppm) of an Astragalus–Atractylodes extract (three replicates per treatment, 40 individuals per replicate) and fed for six weeks. After a 24 h fasting period, crayfish were randomly sampled for subsequent analyses. Results were as follows: (1) There were no significant differences in the final weight, specific growth rate, meat content, hepatosomatic index, intestinal length index, or condition factor among all groups of crayfish (p > 0.05). (2) The crude lipid content in crayfish muscle was significantly lower in all treatment groups compared to the control group (p < 0.05), whereas no significant differences were observed among groups in terms of muscle moisture, crude protein, and ash contents (p > 0.05). (3) Compared with the control group, the activities of glutathione peroxidase (GPX) and catalase (CAT) in the 750 ppm group were significantly increased, while the content of malondialdehyde (MDA) was significantly decreased (p < 0.05). (4) The intestinal microbiota of Procambarus clarkii was dominated by Firmicutes, Proteobacteria, and Actinobacteriota. Dietary Astragalus membranaceus–Atractylodes macrocephala extracts altered community composition, decreasing the relative abundance of opportunistic genera such as Pseudomonas and Mycobacterium and, to some extent, improving co-occurrence network stability. (5) Correlation analyses linked host phenotypes to key differentially abundant genera: final weight was associated with Bosea and Nannocystis, hepatosomatic index and meat content with Nannocystis and Pseudomonas, respectively, and lipase activity with Pseudomonas, Nannocystis, and Bosea (p < 0.05). GPX was associated with Pseudomonas and Mycobacterium (p < 0.05), whereas MDA showed only weak associations with these genera but was negatively correlated with growth performance indices (p < 0.05). Overall, dietary Astragalus–Atractylodes extracts enhanced antioxidant capacity, tended to increase intestinal lipase activity, and significantly altered gut microbial community composition of P. clarkii, including reduced relative abundance of selected putatively harmful taxa and altered inferred microbial association patterns; under the present conditions, 750 ppm produced the most favorable overall response among the tested supplementation levels.

Fishes doi: 10.3390/fishes11090504

Authors: Yudi Herdiana Intan Destianis Hartati Mohamad Natsir Umi Chodrijah Ahmad Syauqi Jafani Regi Darmawan Victor Nikijuluw Rian Prasetia Charles Parningotan Haratua Simanjuntak Viga Ananda Wicaksono Irfan Yulianto

Understanding reproductive dynamics of pelagic fishes is essential for sustainable fisheries management in data-limited tropical systems. This study presents an integrated assessment of the reproductive biology of Katsuwonus pelamis and Decapterus macarellus in Fisheries Management Area 572 (western Indonesia). A total of 1529 individuals (787 individuals of K. pelamis and 742 individuals of D. macarellus) were examined using macroscopic staging with histological validation to characterize gonadal development, size at first maturity, fecundity, and spatial patterns of maturity distribution. Both species exhibited asynchronous ovarian development consistent with batch spawning and extended reproductive activity during the May–July 2025 survey. Estimated L50 = 42.3 cm FL and L95 = 52.5 cm FL for K. pelamis, and L50 = 21.9 cm FL and L95 = 29.0 cm FL for D. macarellus. Batch fecundity increased non-linearly with body size, indicating a disproportionate reproductive contribution of larger females. Mature individuals were recorded in all lunar phases and occurred more frequently in offshore fishing grounds (>12 nautical miles) than in coastal areas. These findings provide region-specific reproductive parameters and spatial maturity information that support size-based management and marine spatial planning in western Indonesian waters.

Fishes doi: 10.3390/fishes11090503

Authors: Manxin Chen Mei Wang Shijie Wu Zhongqi Wang Jihai Gu Zhihua Ni Yuming Zhang

Microplastic pollution severely threatens aquatic ecosystems, yet the trophic microecological risks of petroleum-based polyvinyl chloride (PVC) and biodegradable polyhydroxyalkanoate (PHA) microplastics remain insufficiently compared. This study established a two-trophic food chain model with Daphnia magna and zebrafish to explore the toxic effects and microbial disturbances of environmentally relevant 0.1 mg/L PVC and PHA. A 21-day chronic exposure induced no physiological damage to the survival, growth, reproduction, and locomotion of both organisms, suggesting conventional phenotypic indicators fail to identify early microplastic stress. However, trophic microplastic exposure triggered prominent zebrafish gut dysbiosis with distinct pathogen enrichment patterns. PHA trophic exposure enriched plant pathogenic genera (Acidovorax, Clavibacter, Rhizobium), whereas PVC trophic exposure accumulated zoonotic and clinical pathogens (Acinetobacter, Neisseria, Mycobacterium, Aeromonas). This work verifies that PHA is not entirely eco-safe, and PVC poses greater ecotoxicological risks via trophic pathogen transmission, providing genus-level evidence for differentiated microplastics risk assessment.

Fishes doi: 10.3390/fishes11090502

Authors: Pyungkwan Kim Sena Baek Seonghun Kim

Comparative fishing experiments may include experimental mesh sizes that capture relatively few individuals, resulting in sparsely represented treatments whose influence on selectivity estimation is not well understood. This study evaluated the analytical influence of a sparsely represented experimental mesh on trammel-net selectivity estimates for blackfin flounder (Glyptocephalus stelleri) using complementary parametric (SELECT) and non-parametric generalized additive model (GAM) approaches. Experimental fishing was conducted using five mesh sizes (69, 76, 90, 97, and 121 mm). A complete dataset containing all mesh sizes was compared with a reduced dataset excluding the sparsely represented 121 mm mesh. Model selection, selectivity-curve characteristics, prediction performance, and parameter uncertainty were evaluated using both analytical frameworks. Exclusion of the 121 mm mesh did not change the best-supported model within either framework, and the principal selectivity pattern remained comparatively stable between datasets. Prediction errors increased moderately following exclusion of the sparse observations, while bootstrap analysis indicated substantially greater uncertainty in the secondary binormal component than in the primary component. Differences between datasets were more apparent along the descending limb and upper tail of the selectivity curve, suggesting that the sparsely represented mesh may provide additional information in these less well-represented regions while having little influence on the principal retention region. These findings suggest that the analytical value of sparsely represented experimental treatments should not be assessed solely according to sample size, but also according to their influence on different regions of the selectivity curve. The hierarchical sensitivity framework applied in this study provides a structured approach for evaluating such treatments and may help inform the design and interpretation of future comparative fishing experiments.

Fishes doi: 10.3390/fishes11090501

Authors: Jun Du Wenhao Liao Bo Yan Xinhui Dai

The global ‘Blue Transition’ presents a critical policy dilemma for marine fisheries: how to achieve ecological sustainability and carbon neutrality while maintaining socio-economic vitality. This study addresses this challenge by analyzing the complex interplay between the ecological, social, and economic systems within China’s marine fisheries. Our research purpose is to identify effective governance pathways for a coordinated and sustainable transition. We developed a system dynamics model, informed by panel data from 2010–2022, to simulate the long-term outcomes of different policy scenarios. This approach allows us to move beyond static analysis and understand the dynamic feedback mechanisms that shape the fishery sector. Our analysis of historical data reveals that the overall system coordination improved initially but has since stagnated at a basic level. The most significant outcome of our simulations is the identification of the social system—encompassing technological innovation, governance, and human capital—as the central lever for progress. Our findings demonstrate that policies focused narrowly on either economic growth or ecological restoration are suboptimal. The optimal path to high-quality, sustainable development is an integrated strategy that prioritizes investment in the social system to mediate the conflict between economic and ecological goals. This provides a crucial insight for marine policy, suggesting that effective governance frameworks are the key enablers of a successful Blue Transition.

Fishes doi: 10.3390/fishes11090500

Authors: Shuai Han Sitong Wang Haopeng Hu Wenping Yang Shuo Qin Peng Gao Yanming Sui Yebing Yu Mei Jiang Lei Li

Thermal elevation and residual chlorine pollution are two anthropogenic stressors that co-occur in estuarine waters affected by coastal power plant effluents. A 30-day exposure experiment was established with six treatment combinations comprising three temperatures (27 °C, 28 °C, and 30 °C) and two residual chlorine concentrations (0 mg/L and 0.02 mg/L) on Meretrix meretrix. Sampling was conducted on days 0, 10, 20 and 30 of the trial. The results indicated that elevated temperature (30 °C) significantly suppressed shell height and total body weight, while residual chlorine (0.02 mg/L) exerted time-dependent effects on shell length and width, with a significant interactive effect on shell length only at day 30. Crude lipid content declined with increasing temperature and residual chlorine exposure, whereas moisture and ash contents showed significant two-way interactions at all sampling time points. Intestinal amylase activity was continuously regulated by both stressors, with interactive responses on days 10 and 20, and was significantly suppressed under combined high temperature and residual chlorine stress. Collectively, we infer that combined exposure to elevated temperature and residual chlorine impairs shell growth, muscle biochemical composition and intestinal amylase activity of M. meretrix. Long-term experiments are required to further clarify the joint toxic effects of thermal stress and residual chlorine on the clam species.

Fishes doi: 10.3390/fishes11090499

Authors: Dong Wang Xiangyu Long Zengguang Li Rong Wan Tiejun Li Yuanming Guo Pengbo Song

Estuaries support distinct spawning and nursery habitats for migratory fishes, yet the differential environmental response patterns between these two critical early life habitats remain poorly understood from a spatial non-stationarity perspective. Based on six ichthyoplankton surveys conducted during peak and late spawning seasons from 2018 to 2020 in the Yangtze Estuary, this study applied geographically weighted regression (GWR) models to quantify the spatially varying effects of sea surface temperature, sea surface salinity, chlorophyll-a, water depth and distance to coast on the distributions of Coilia mystus eggs and larvae. The results reveal clear divergence in both spatial pattern and environmental drivers between spawning and nursery habitats. Spawning grounds were persistently concentrated in the middle reaches of the South Branch, and shifted approximately 10 km upstream during the spring saltwater intrusion event in 2020. Nursery grounds, by contrast, formed a stable dual-core structure, with the northern core at the North Branch mouth consistently supporting higher larval densities than the southern core in the North and South Passages. Salinity was the primary limiting factor for spawning in spring, while temperature dominated in summer, and chlorophyll-a was never retained in optimal egg models. For larvae, chlorophyll-a emerged as a consistent key driver alongside salinity and temperature, and local regression coefficients spanned a wider range than those for eggs, indicating greater spatial heterogeneity in larval distribution–environment relationships. This study provides the first comparative analysis of spatially non-stationary environmental controls on spawning versus nursery habitats of C. mystus, and offers empirical support for stage-specific habitat conservation and fisheries management in the Yangtze Estuary.

Fishes doi: 10.3390/fishes11090498

Authors: Weiwei Lv Muyan Li Yuxuan Gao Wei Hu Mingyou Li Wenzong Zhou

The rice field eel (Monopterus albus) is an economically important aquaculture species widely distributed in Southeast Asia. However, the lack of nationally approved varieties and the increasing demand for high-quality eel products have highlighted the necessity of developing improved germplasm resources for aquaculture production. In this study, morphometric morphology and muscle texture traits were evaluated in 367 wild eel individuals, and a genome-wide association study (GWAS) based on whole-genome resequencing was conducted to identify genetic variants and candidate genes associated with economically important traits, including body length (BL), tail length (TL), tail height (TH), head length (HL), head width (HW), head height (HH), hardness, chewiness, springiness, and resilience. The GWAS identified three significant and seventeen suggestive SNPs associated with body shape traits, with most loci located on chromosome 4. Candidate gene analysis of the associated genomic regions revealed several candidate genes potentially associated with growth regulation, nutrient metabolism, and skeletal development, including b4galnt4a, tmem86a, cpt1b, mrpl23, lama1, gcm2, wnt3a, thrab, and bmpr1a. Additionally, four suggestive SNPs associated with muscle texture traits were detected, and candidate genes related to muscle development and extracellular matrix regulation, including fstl1b, col5a3a, and pnn, were identified. These findings provide new insights into the genetic basis underlying morphometric variation and muscle texture diversity in M. albus. The identified SNP markers and candidate genes provide potential molecular resources for understanding the genetic basis of body morphology and muscle texture variation in rice field eel.

Fishes doi: 10.3390/fishes11090497

Authors: Chuanqi Yu Wenlu Zhu Wenjun Wang Wenqiang Xu Yu Liu Xingtian Cai Yanfa Xu Defu Yang Zhuqing Yang Zirui Wang Qiubai Zhou Haohua He

This study aimed to evaluate rice yield attributes, loach Paramisgurnus dabryanus muscle quality, and soil biochemical composition under rice monoculture (RM), rice–loach coculture (RLC), and loach monoculture (LM). This trial was conducted for 90 days, and then rice, fish muscle and soil were obtained for analyses. The results showed that there were no significant differences in rice yield attributes between the rice–loach coculture (RLC) and rice monoculture (RM) groups. However, rice–loach coculture (RLC) improved muscle quality-related parameters, including increased hardness and springiness of loach muscle. Meanwhile, muscle metabolomic analysis showed that all the differentially expressed metabolites (DEMs) in the significantly enriched pathways of lysine degradation and lysine biosynthesis were up-regulated in the rice–loach coculture (RLC) group compared with the loach monoculture (LM) group. Furthermore, the rice–loach coculture (RLC) improved soil physicochemical properties, including an increase in microbial biomass nitrogen (MBN) content and activities of soil N-acquiring enzymes (NAG and LAP). Moreover, soil microbiome analysis showed that the abundance of Candidatus Koribacter versatilis, Acidobacteria bacterium WX27 and Pseudolabrys taiwanensis was significantly increased in the rice monoculture (RM) and rice–loach coculture (RLC) groups compared with the loach monoculture (LM) group. Pairwise Spearman’s correlation analysis of the top 30 soil microbial species and soil physicochemical properties indicated that Terrimonas sp. H1YJ31 showed a highly significant positive correlation with the soil N-acquiring enzymes (N-acetylglucosaminidase, NAG; leucine aminopeptidase, LAP) and a soil C-acquiring enzyme (exo-β-1,4-glucanase C1), whereas Gaiella occulta, Methyloceanibacter marginalis and Anaerohalosphaera lusitana had a highly significant negative correlation with S-NAG, S-LAP and S-C1. In short, the improved fish muscle quality and soil biochemical composition were ascribed to the increased hardness and springiness of loach muscle and the abundance of soil Terrimonas sp. H1YJ31.

Fishes doi: 10.3390/fishes11090496

Authors: Hemilly Cristina Menezes de Sá Isabela Thaiane Vieira Santos Mikaelly Ferreira Miranda Paulo Edson Camilo Mol de Oliveira Guilherme Campos Tavares Daniela Chemim de Melo Hoyos Luciano Soares de Lima

Ornamental aquaculture represents a high-value segment of global aquaculture and plays an important role in income diversification for small-scale producers. Despite its economic relevance, investment decisions in ornamental fish farming are often supported by limited economic information and rarely incorporate risk and uncertainty into economic assessments. This study developed and applied a stochastic framework to evaluate the economic performance and investment risk of intensive ornamental aquaculture using Betta splendens production as a representative case study. A representative production system was developed from technical and economic surveys conducted on 20 commercial family operated farms located in one of Brazil’s major ornamental fish production clusters. The production system comprised three greenhouse units with an estimated annual output of 162,288 marketable fish. Production costs were estimated using conventional cost-accounting procedures, whereas economic risk was assessed through Monte Carlo simulation incorporating uncertainty in biological, productive, and market variables. The estimated total production cost was US$0.14 fish−1, while the weighted average selling price reached US$0.18 fish−1, resulting in a benefit–cost ratio of 1.33, a profitability of 25.09%, and an annual return on invested capital (ROIC) of 23.90% under the deterministic baseline scenario. Monte Carlo simulation estimated a mean annual ROIC of 22.46%, with a 98.53% probability of positive economic returns. Sensitivity analysis identified labor demand, the selling price of premium males, and reproductive productivity as the principal drivers of economic risk. The results indicate that economic returns in B. splendens farming are primarily influenced by managerial efficiency, labor requirements, and market conditions rather than production volume alone. The proposed framework provides a robust tool for evaluating economic viability and investment risk in ornamental fish farming under uncertainty and may support decision-making in small-scale aquaculture systems.

Fishes doi: 10.3390/fishes11090495

Authors: Antonio Rafael Rodríguez Abraham Hugo Daniel García Juárez Carlos Enrique Mendoza Ocaña Ingrid Estefani Sánchez García Guillermo Paris Arias Pereyra

This study examines the long-run relationship between terms of trade (TOT) and real fishing-sector GDP in a small open economy, focusing on the Peruvian case. Despite the strategic importance of fisheries for exports, employment and foreign exchange generation, the extent to which external price conditions are associated with fishing-sector performance remains insufficiently explored in sector-level research. Building on the notion that TOT summarise opportunities and constraints arising from the international environment, the paper evaluates whether persistent external conditions are linked to the long-run trajectory of the fishing sector. The analysis employs the Johansen cointegration approach and a bivariate Vector Error Correction Model (VECM) using quarterly data for the period 2001–2025. Seasonal effects are incorporated through quarterly dummy variables, while robustness is assessed by controlling for extreme El Niño–Southern Oscillation (ENSO) episodes and the COVID-19 pandemic. The results reveal the existence of a unique long-run equilibrium relationship between TOT and fishing-sector GDP. The error-correction mechanism indicates that deviations from equilibrium are actively corrected over time, whereas the adjustment coefficient for TOT is statistically insignificant. Robustness tests further show that El Niño episodes are negatively and significantly associated with short-run sectoral performance, while no statistically significant association is detected for La Niña. The COVID-19 control does not materially alter the long-run relationship identified by the model. The findings contribute sector-level evidence for a resource-dependent economy and suggest that long-run equilibrium and sectoral adjustment dynamics are important elements for understanding the long-run behaviour of the fishing sector.

Fishes doi: 10.3390/fishes11090494

Authors: Sheng Zeng Jinli Hu Qinglan Zhou Feng Chen Ning Qin Zhou Zhou Xianbo Zhang

The microphthalmia-associated transcription factor (Mitf) family is central to melanocyte biology. Teleosts possess two mitf paralogs, mitfa and mitfb, yet their functional divergence remains incompletely understood. Here, we characterized the coding sequences, phylogeny, tissue distribution, developmental expression, cellular localization, and stress responsiveness of mitfa and mitfb in Congjiang natural mutant crucian carp (NMCC). Both genes encoded proteins containing the characteristic bHLH-ZIP domain. Phylogenetic analysis revealed that teleost mitfb clustered with the tetrapod mitf clade, indicating closer evolutionary affinity than mitfa. mitfa was predominantly expressed in skin and eyes, whereas mitfb showed broad tissue distribution. Both paralogs were constitutively expressed in skin across developmental stages; mitfa levels remained consistently lower than mitfb. Both transcripts were localized to melanocyte-containing regions of the skin. Transcriptomic analysis following high temperature (34 °C), UV radiation, and combined stress (48 h) revealed that mitfa was significantly upregulated by thermal stress, while mitfb showed no significant changes. Profiling of DNA damage response pathways uncovered extensive, stress-specific transcriptional remodeling. High temperature broadly suppressed apoptotic genes while upregulating tsc2, gadd45b, and cdip1; UV triggered widespread apoptotic gene activation. Combined stress elicited a hybrid signature. Notably, robust DNA Damage Response pathway remodeling contrasted with muted mitf responses, suggesting that DNA Damage Response-to-pigmentation signaling may operate predominantly at post-transcriptional levels. These findings reveal a substantial regulatory divergence between mitfa and mitfb, with mitfa maintaining a conserved melanogenic role while mitfb has been co-opted for broader functions in non-pigmentary tissues. The differential stress responses of the two paralogs further provide new insights into tissue-specific genotoxic stress signaling and melanogenic regulation in teleosts.

Fishes doi: 10.3390/fishes11080493

Authors: Bupebe Júlio Sanca Diosnes Manuel Nonque Félix Guillaume Wilfred Boa Morte Zacarias Jeremias Francisco Intchama Gui Manuel Machado Menezes

Pseudotolithus elongatus is one of the most commercially important species supporting artisanal fisheries in Guinea-Bissau; however, its population biology and reproductive characteristics remain poorly understood, particularly in estuarine ecosystems. This study provides the first integrated biological characterisation of P. elongatus in the Cacine River Estuary, Guinea-Bissau, based on 1776 specimens collected through three independent sampling programmes. Length at first sexual maturity (L50) was estimated using binomial generalised linear models (GLMs); length–weight relationships were assessed by ordinary least squares regression and analysis of covariance (ANCOVA); sexual size dimorphism was evaluated using a battery of parametric and non-parametric tests (ANOVA, Welch’s t-test, Kruskal–Wallis, Kolmogorov–Smirnov); and sex ratio was tested using chi-square goodness-of-fit tests with Yates’ continuity correction. Females attained sexual maturity at a significantly smaller size than males (L50 = 224.9 mm vs. 306.8 mm), and both sexes exhibited positive allometric growth. Females attained larger body sizes and predominated in the largest length classes, confirming pronounced sexual size dimorphism. Reproductive activity occurred throughout the year, with a distinct spawning peak during the dry season (February–April), and the overall sex ratio remained close to parity despite significant variation among length classes and months. These findings provide a biological baseline to support evidence-informed fishery management of P. elongatus in Guinea-Bissau and highlight the need for long-term, standardised monitoring in the Cacine River Estuary.

Fishes doi: 10.3390/fishes11080492

Authors: Roxani Naasan Aga-Spyridopoulou Kyriaki Pyloridou Martina Ciprian Ilektra Athinaiou Stelios Katsanevakis Dimitrios K. Moutopoulos Ioannis Giovos

The Greek seas have hosted a diversity of sharks and rays since antiquity, with Aristotle providing the earliest detailed descriptions in his History of Animals, while the first modern documented record dates back to 1858. Despite this long history of attention and the acceleration of research on elasmobranchs over the past two decades, information on their spatial distribution remains fragmented, with most studies focusing on biological and fisheries-related parameters at low taxonomic and/or spatial resolution. This is concerning given that over 50% of Mediterranean chondrichthyans are now threatened with extinction. The present study reconstructs the distribution of extant species in the Greek seas by integrating published literature, mass and social media, biodiversity platforms, citizen science programs, research projects, and national datasets. Although records were compiled from 1858 onwards, only those starting from 1942 contained sufficiently precise locality information to be georeferenced. The review yielded 5596 spatial presence records of initially 67 species; however, after data validation, 62 species were confirmed: 33 shark species, 28 batoid species, and 1 chimaera species, of which 54.8% were from research programs, 30.5% were from published research, and 14.4% were from citizen science and were previously unpublished. These records enrich knowledge of threatened and data-deficient taxa and may serve as a useful baseline for future analyses and distribution modeling, as well as for informing marine spatial planning and conservation prioritization efforts in the eastern Mediterranean.

Fishes doi: 10.3390/fishes11080491

Authors: Chao Guo Deqi Sun Ben Yang Chenyu Shi Shikai Liu

In recent years, aquaculture, a critical pillar of global food security, has faced challenges including germplasm resource degradation, frequent disease outbreaks, and insufficient environmental adaptability. To address these issues, omics technologies—centered on genomics, transcriptomics, and related fields—are driving the transformation of aquaculture toward precision and intelligence by establishing a three-dimensional “genotype–phenotype–environment” knowledge network. In this review, we outline foundational applications of omics in aquaculture and highlight the characteristics and current applications of distinct omics approaches. Furthermore, we summarize three core application domains of omics in aquaculture: (1) genetic breeding via genomic selection (GS), gene editing, and multi-omics molecular dissection of economic traits; (2) disease prevention through host–pathogen interaction studies and microbial engineering; and (3) environmental assessment through multi-omics characterization of biological and ecological responses. Additionally, we identify challenges in applying omics technologies to aquatic breeding and database development. Overall, this review aims to provide aquaculture practitioners with actionable insights by enhancing understanding of omics-driven innovations in sustainable aquaculture advancement.

Fishes doi: 10.3390/fishes11080490

Authors: Xiaoye Ni Xuan Zhang Ping Zhuang Lei Liu Rongrong Ma

Portunus trituberculatus is an economically important marine crab species in China. Short-term nutritional conditioning during the juvenile stage may improve their physiological readiness before release. This study compared the effects of four dietary treatments on the growth, antioxidant capacity, immune function, and hepatopancreatic transcriptome of juvenile P. trituberculatus. A 4-week feeding trial compared a commercial pelleted diet (Treatment C) with three natural marine diets: Larimichthys crocea (Treatment Y), Litopenaeus vannamei (Treatment X), and Ruditapes philippinarum (Treatment B). The results demonstrated that Treatments X and B exhibited optimal growth performance, with significantly higher weight gain rate (WGR) and specific growth rate (SGR) than Treatments Y and C (p < 0.05). Regarding immune and antioxidant functions, Treatment X showed significantly enhanced parameters, including total antioxidant capacity (T-AOC) and activities of superoxide dismutase (SOD) and catalase (CAT), as well as contents of reduced glutathione (GSH) and lysozyme (LZM), all of which were markedly higher than those in Treatment C (p < 0.05). Transcriptomic analysis further revealed the molecular mechanisms underlying these physiological enhancements. Compared to the control, Treatment X exhibited significant enrichment in immune-related pathways, specifically the phagosome and gap junction signaling pathways. Notably, key cytoskeleton-related genes (tubulin alpha chain and tubulin beta chain) were significantly up-regulated, suggesting that the shrimp diet enhances cellular immunity by promoting cytoskeletal remodeling and phagocytosis efficiency. In contrast, Treatment B mainly showed enrichment in lysosome and amino sugar metabolism pathways.

Fishes doi: 10.3390/fishes11080489

Authors: Jung-Mo Jung Bong-Jin Cha Kyu-Suk Choi Min-Seuk Park Myounghee Kang Hyun-Young Kim

Marine mammal Bycatch Reduction Devices (BRDs) can result in the escape of target fish species. In the present study, a modified single-layer codend configuration developed from previous studies was evaluated using BRDs with guide net angles of 30° and 45°. Catch was collected separately from the codend and the BRD cover to estimate catch loss rates and characteristics. For caught species, catch loss rates based on the number and weight of individuals were 9% and 13% for herring with the 30° guide net and 16% and 18% with the 45° guide net, respectively. For Korean pomfret, catch loss rates were 24% and 23% at 30° and 4% at 45°. These results suggest that further modification of BRD is necessary. In contrast, catch loss rates of mackerel with the 30° guide net reached 56%, whereas hairtail showed loss rates of 60% and 65% with the 45° guide net. Underwater observations indicated that catch loss was influenced by swimming behavior and entanglement with the guide net. Despite the modification of the codend to a single layer, the present study still observed high catch loss rates. However, no bycatch of marine mammals occurred during the experimental operations.

Fishes doi: 10.3390/fishes11080488

Authors: Allie N. Burdette-Lapuz Malachi R. Hubbard Cameron M. Emadi Preston T. Bean Edward M. Mager

Culvert construction at stream crossing sites can lead to zones of high-velocity water flow which can disrupt the dispersal and connectivity of species of greatest conservation need (SGCN) in Texas. To help inform effective culvert design, the swimming performance of the following seven fish species has been measured, the first three of which are SGCN themselves, and the last four serve as hosts for glochidia of SGCN mussels (mussel genera indicated in parentheses): Colorado Roundnose Minnow, Texas Shiner, Headwater Catfish, Largemouth Bass (host for Lampsilis spp.), Green Sunfish (host for Lampsilis spp.), Channel Catfish (host for Cyclonaias spp.) and Blacktail Shiner (host for Fusconaia spp.). The primary objective was to measure the critical swimming speeds (Ucrit) under a range of relevant temperatures (15, 22.5, and 30 °C) to be used in site-specific calculations of culvert water velocities (Vf). A secondary objective was to collect additional physiological endpoints of relevance to overall swimming performance, including maximum burst swimming speed (Umax), metabolic rate measurements (i.e., standard (SMR), maximum (MMR) and aerobic scope (AS)) and calculations of cost of transport (COT) and optimal swimming speed (Uopt). As expected, Ucrit tended to increase with increasing temperature for several species with metabolic rate measurements following congruent trends, whereas Umax exhibited thermal independence for all species.

Fishes doi: 10.3390/fishes11080487

Authors: Xinyu Ai Junjie Wu Shengmao Zhang Na Lin Banghong Wei Quanyou Guo

Large yellow croaker (Larimichthys crocea) is an economically important marine fish, yet rapid and non-destructive discrimination between sea-caught and farmed collection-source groups remains challenging. This study developed a fish-level analytical workflow integrating YOLO11n-seg instance segmentation with visible–near-infrared hyperspectral imaging to extract relative reflectance ratios from six anatomical regions. The analytical cohort comprised 258 unique fish, including 171 sea-caught and 87 farmed individuals. Source categories were assigned according to the original capture or cage-culture collection channels. Fish identity was used as the grouping unit in five-fold internal cross-validation, and classification performance was evaluated based on out-of-fold fish-level predictions. Logistic-regression models achieved AUC values ranging from 0.985 to 1.000 across the six individual anatomical regions. The combined six-region model achieved an accuracy of 0.996 (95% CI, 0.988–1.000) and an AUC of 1.000 (95% CI, 1.000–1.000) within the present cohort. For anatomical-region segmentation, the 20-image validation set contained 140 annotated instances. Bounding-box precision, recall, mAP@0.5, and mAP@0.5–0.95 were 0.976, 0.983, 0.981, and 0.700, respectively, while the corresponding mask metrics were 0.969, 0.976, 0.972, and 0.669. These results indicate that region-specific hyperspectral information can support highly accurate internal discrimination between the two collection-source groups and provide an interpretable basis for characterizing source-associated spectral differences. However, the source labels were not independently verified, potentially influential covariates were incompletely recorded, and no independent external cohort was available. Therefore, the present findings should be interpreted as internally validated collection-source discrimination rather than verified provenance authentication or evidence of external generalizability.

Fishes doi: 10.3390/fishes11080485

Authors: Hua Jiang Yufei Ji Zhiqi Zhang Yongxiang Yu Chunyuan Wang Yingeng Wang Xiaojun Rong Aijun Ma Shuyi Li Zheng Zhang

Photobacterium damselae subsp. damselae (PDD), a marine fish pathogen, has an unclear contribution of tonB genes to iron acquisition and pathogenicity. ΔtonB1-PDD and ΔtonB2-PDD mutants as well as their complemented strains were generated via homologous recombination from the virulent strain PDD1605. Growth was evaluated by monitoring OD600 with viable-count calibration, intracellular iron was measured using a colorimetric assay, biofilm was detected by crystal violet staining, transcription was analyzed through qRT-PCR, and pathogenicity was assessed via an 8-day intramuscular challenge in black rockfish (Sebastes schlegelii). Under iron limitation induced by 100 μM 2,2′-dipyridyl, the maximum density decreased from 4.51 × 108 CFU/mL in wild-type (WT-PDD) to 4.00 × 108 and 3.64 × 108 CFU/mL in ΔtonB1-PDD and ΔtonB2-PDD respectively, and was largely restored after complementation. The intracellular iron content declined from 3.75 × 10−4 ± 4.00 × 10−6 nmol/106 cells in WT-PDD to 3.13 × 10−4 ± 1.05 × 10−5 nmol/106 cells in ΔtonB1-PDD and 2.55 × 10−4 ± 2.00 × 10−5 nmol/106 cells in ΔtonB2-PDD. Compared with WT-PDD, biofilm formation was reduced by 22.1% in ΔtonB1-PDD and by 24.8% in ΔtonB2-PDD. Deletion of tonB2 induced mild yet statistically significant transcriptional alterations in multiple iron acquisition and virulence-related genes, while colony morphology, swarming motility, hemolysis, phospholipase activity, biochemical traits, and antimicrobial susceptibility remained unchanged. In the high-dose challenge assay, WT-PDD caused 100% mortality within 2 days, whereas ΔtonB1-PDD and ΔtonB2-PDD caused 17/20 and 18/20 deaths respectively; all infected groups reached 100% mortality by day 3. In the low-dose challenge assay, WT-PDD, ΔtonB1-PDD, and ΔtonB2-PDD caused 12/20, 12/20, and 13/20 deaths by day 2, with cumulative mortalities reaching 80%, 70%, and 80% by day 8, respectively. Kaplan–Meier analysis detected no significant differences among the survival curves at either challenge dose. These findings suggest that tonB1 and tonB2 play roles in iron acquisition, low-iron adaptation, and biofilm formation, with tonB2 deletion exerting greater effects on growth and intracellular iron accumulation under iron-limited conditions.

Fishes doi: 10.3390/fishes11080486

Authors: Yuting Ding Xizhao Zhang Yanfeng Zhou Dian Fang Jia Yuan Yang You

Neosalanx taihuensis is a fish species endemic to China, primarily distributed in the middle and lower reaches of the Yangtze and Huaihe rivers and their affiliated lakes. To assess its resource status and facilitate targeted conservation of genetic diversity, we analyzed genetic differences among populations in the lower Yangtze River. Samples were collected from four natural river populations (JJ, AQ, NJ, and TZ) and one lacustrine population (THL). Whole genome resequencing was performed to characterize genetic diversity, population structure, and selection signatures across the five populations. The results showed no obvious genetic divergence among the natural river populations, whereas all natural river populations were distinctly separated from the THL population. The natural river populations harbored higher genetic diversity than the THL population. Gene flow analysis suggested that historical gene exchange might have occurred between TZ and THL, as well as between TZ and NJ. Selective sweep analysis identified Chr01, Chr04, Chr09, and Chr15 as candidate genomic regions potentially carrying adaptive selection signatures. In summary, conservation efforts should prioritize the genetic diversity of both natural river populations and the THL population, facilitate gene flow among populations, and adopt differentiated management strategies for each group.

Fishes doi: 10.3390/fishes11080484

Authors: Wei Chen Chunfang Wang Shiyun Chi Guangbin Gao Zhongguan Jiang Yang Wang Zhe Leng Mi Wei Xianfu Zhao Peiming Ma

It is imperative that freshwater fish biodiversity research incorporates diverse components, encompassing taxonomy, phylogeny and function, alongside multifaceted facets, including richness, divergence and regularity. This comprehensive approach is essential to facilitate a more profound comprehension of freshwater ecosystem functions, to elucidate the mechanisms underpinning fish community assembly, and to accurately assess the impacts of anthropogenic disturbance. Consequently, this scientific understanding can inform the development of effective fish conservation and ecosystem management strategies. This study utilized environmental DNA metabarcoding to assess the diversity of fish across the entire Yangtze River, encompassing the upper reach (Upper), the Three Gorges Reservoir area (RES_SX), and the downstream reach (Down). The results indicated that 150 distinct fish species were detected, with the RES_SX area exhibiting a significantly lower taxonomic diversity and fish detection rate in comparison to the other two regions. Conversely, phylogenetic and functional diversity exhibited stability post-normalization by taxonomic richness. Furthermore, investigation of the divergence facet of alpha-diversity demonstrated a reduction in clustering and an improvement of overdispersion on the phylogenetic and functional diversity, respectively, in the RES_SX and Down regions. Beta-diversity analysis further revealed lower taxonomic beta-diversity but higher phylogenetic and functional beta-diversity in the RES_SX area. A substantial degree of geographic distance-dependent similarity was identified for all three components of beta-diversity in the Upper Reach. Conversely, these components were found to be disrupted in the Down Reach. Finally, an analysis of the assembly mechanism revealed stochastic processes, dispersal limitation and drift as the dominant factors shaping the fish communities, with reduced dispersal limitation in the RES_SX area. This study provides novel insights into the multidimensional diversity of fish populations in response to dam construction, emphasizing the necessity of integrating multiple facets of diversity for accurate impact assessment and supporting evidence-based conservation of fish species in the Yangtze River.

Fishes doi: 10.3390/fishes11080483

Authors: Yan-Lun Wu Po-Yuan Hsiao Yonatan Isai Valladares Ponce Sunardi Sunardi Aloysius Dimas Sanjaya Saliyo Li-Xiang Li Kuo-Wei Lan

Offshore wind farm (OWF) development raises concerns regarding potential conflicts with local fisheries and marine ecosystems. This study investigated the spatiotemporal dynamics of gillnet and trawl fisheries in the coastal waters off Changhua, Taiwan, across various development phases. (2016–2024). Spatial analysis revealed distinct operational patterns: gillnet fleets operated within and adjacent to wind farms, while trawl activities were concentrated in northern offshore waters, largely avoiding the development zone. The gillnet fishery demonstrated a significant increase in Income Per Unit Effort (IPUE), suggesting that local fishers successfully employed adaptive strategies. The IPUE of the trawl fishery indicated a slightly lower value during this period. These findings indicate that current OWF development has historically coexisted with gillnet fisheries without causing economic loss. The catch composition of gillnet fisheries remained stable, dominated by Silver croaker and Pharaoh cuttlefish. The species diversity indices of both fisheries showed a stable to increasing trend driven by seasonal variability rather than construction impacts. The habitat-driven shift in community structure was observed within the wind farm zone (gillnet fisheries), where the dominance of benthic species (e.g., Flatfish) transitioned toward reef-associated taxa (e.g., Spotted catfish, Black Sea bream). This indicates that the turbine foundations may function as artificial reefs, supporting a more complex assemblage. Nevertheless, the observed habitat alterations highlight the necessity for long-term monitoring to ensure the sustainable symbiosis of renewable energy expansion and marine resource conservation.

Fishes doi: 10.3390/fishes11080482

Authors: Anqi Pang Wen Yan Xuying Jia Dan Zhang Peng Shao Wenli Zhou

Aqueous Chlorella extract (CE) is a functional feed additive derived from widely cultivated microalgae. It is rich in proteins, polysaccharides, pigments, polyunsaturated fatty acids, vitamins and other bioactive compounds. CE possesses great potential to improve the health status and physiological performance of aquatic animals. This study investigated the effects of dietary CE on inflammatory response, non-specific immunity, antioxidant capacity, lipid metabolism, immune gene expression, intestinal histomorphology and intestinal microbiota in Litopenaeus vannamei. Shrimp were fed diets containing 0%, 1%, or 5% CE for 60 days. The 1% CE treatment produced stronger responses in several non-specific immune and antioxidant-related indicators and induced broader changes in immune-related gene expression. In contrast, the 5% CE treatment showed more pronounced changes in inflammation-related factors, lipid metabolism, and intestinal morphology. CE supplementation also altered intestinal microbial composition and predicted microbial functions, with different response patterns between the two inclusion levels. A distinctive feature of this study is the integrated identification of inclusion-level-specific response patterns across host physiological and intestinal microbial endpoints, rather than a simple increase in effects with increasing CE inclusion. Overall, the 1% treatment was more closely associated with immune and antioxidant-related responses, whereas the 5% treatment was more closely associated with anti-inflammatory, lipid-regulatory, and intestinal effects. These findings demonstrate the potential of CE as a functional aquafeed additive for improving aquatic animal health and provide a scientific basis for its application in sustainable shrimp aquaculture.

Fishes doi: 10.3390/fishes11080481

Authors: Fuyong Huang Kefan Guo Xiao Liang Lun Qian Jinyu Tang Qinghua Jiang Lina Jiang Jubin Xing Yu Zhang Qingman Yang

Farming models profoundly influence the biological traits of aquatic organisms. This study compared muscle nutrients, muscle transcriptome, and gut microbiota of Pelodiscus sinensis reared under rice-field and pond conditions. Compared with the pond group (Group P), the rice-field group (Group R) exhibited significantly lower linoleic acid (LA) and higher arachidonic acid (ARA), indicating an altered muscle fatty acid profile. Transcriptomic analysis further showed that differentially expressed genes were mainly involved in fatty acid metabolic processes. For gut microbiota, Group R had a higher relative abundance of Firmicutes_C at the phylum level, and Acidaminococcus was uniquely detected at the genus level. These findings reveal that rice-field culture drives distinct muscle fatty acid profiles and gut microbial characteristics in P. sinensis, providing a theoretical basis for understanding the effects of rice-field culture on turtle nutrition and intestinal health.

Fishes doi: 10.3390/fishes11080480

Authors: Ning Fu Mengxin Xing Yuyu Wang Linwei Yang Di Wang Taolin Fan Bang Xiao Shengwen Niu

C-type lectins (CTLs) are important pattern recognition receptors (PRRs) involved in innate immune defense in crustaceans. In this study, a novel C-type lectin, designated LvCTL, was identified and functionally characterized from Litopenaeus vannamei. Sequence analysis revealed that the open reading frame (ORF) of LvCTL is 495 bp in length and encodes a 164-amino acid polypeptide containing a typical C-type lectin-like domain but lacking the classical carbohydrate-binding motifs. Notably, two novel EPF motifs were identified in the CTLD region, suggesting a potential non-canonical ligand recognition pattern. Phylogenetic analysis revealed that LvCTL clustered with other crustacean CTLs. Tissue expression analysis revealed that LvCTL exhibited the highest transcript level in the hepatopancreas. After immune stimulation, LvCTL expression in the hepatopancreas was significantly regulated by LPS, Vibrio parahaemolyticus, Staphylococcus aureus, WSSV and Poly(I: C), indicating its involvement in antimicrobial immune responses. RNA interference assays showed that knockdown of LvCTL significantly increased the bacterial burden and reduced the survival rate of shrimp after V. parahaemolyticus infection. Furthermore, recombinant LvCTL displayed broad bacterial binding activity to Gram-negative and Gram-positive bacteria and induced calcium-dependent agglutination of V. parahaemolyticus and S. aureus. Taken together, these results demonstrate that LvCTL functions as an important immune recognition molecule and contributes to antibacterial defense against V. parahaemolyticus in L. vannamei. These findings broaden our understanding of the functional diversity of shrimp CTLs and their contributions to crustacean innate immunity.

Fishes doi: 10.3390/fishes11080479

Authors: Yanming Sui Jingtao Liu Haopeng Hu Yan Ji Yuanhao Ren Bo Qin Na Ying Tingting Lin Siping Li Hanfeng Zheng Lei Li

Using a three-factor orthogonal design, we investigated the transcriptomic and histological responses of triploid rainbow trout (Oncorhynchus mykiss) gills across three salinities (10, 20, and 30 ppt) over 60 days, with temperature and body size as background conditions. Results showed that 20 ppt was associated with extensive transcriptional reprogramming, with 3333 differentially expressed transcripts (DETs), whereas 30 ppt induced only 120 DETs; WGCNA further identified salinity-correlated modules involved in ion transport and ribosome biogenesis. Histological alterations remained within physiological ranges with no salinity-dependent severity gradient, as confirmed by semi-quantitative scoring. These findings demonstrate that triploid rainbow trout gills employ distinct molecular strategies at medium versus high salinity. Within the 10–30 ppt range examined, 20 ppt was the salinity at which transcriptional reprogramming was most active, suggesting that this intermediate salinity warrants further investigation as a potential acclimation stage.

Fishes doi: 10.3390/fishes11080478

Authors: Zhongquan Jiang Sijia Wu Yong Zheng Di Peng Siping Li Yuanhao Ren Bo Qin Hanfeng Zheng Lei Li Tingting Lin

Rainbow trout (Oncorhynchus mykiss) is an important cold-water aquaculture species and a tractable salmonid model for functional genomics. Rapid advances in chromosome-level genome assemblies, genetic variation resources, regulatory annotations, tissue and cell models, controlled challenge systems, and genome-editing technologies have established an increasingly integrated framework for linking genomic variation with measurable phenotypes. Evidence from studies of mucosal immunity, disease-resistance genetics, and environmental stress responses indicates that these resources can improve candidate-gene prioritization and mechanistic interpretation across molecular, cellular, tissue, and whole-fish levels. However, differential gene expression, quantitative trait locus and genome-wide association signals, genomic predictions, and cell-type localization remain largely associative and rarely provide direct evidence of causality. Interpretation is further complicated by salmonid-specific whole-genome duplication, because retained paralogues may exhibit tissue-specific divergence, functional redundancy, and compensatory responses. Further progress will require the integration of pangenomics, regulatory annotation, single-cell and spatial analyses, and paralogue-aware functional perturbation in both cell-based and whole-fish systems. Such integration will strengthen causal inference, clarify genotype–phenotype relationships, and support disease-resistant breeding, healthy aquaculture, and environmental risk assessment.

Fishes doi: 10.3390/fishes11080477

Authors: Yan Jiang Zhixin Jin Yongjiang Xu Aijun Cui Jichang Zheng Xin Cai Zhiyong Xue

Copper nanoparticles (Cu-NPs) are widely used in aquaculture for their growth-promoting and immunoenhancing properties. However, excessive or over-accumulated Cu-NPs in aquaculture water cause toxicity through waterborne immersion. To explore the toxicity effects of waterborne Cu-NPs on yellowtail kingfish (Seriola aureovittata), a 7-day exposure experiment comprising a control group (no Cu-NPs), a low-concentration group (0.120 mg/L), and a high-concentration group (0.384 mg/L) was conducted, followed by a 7-day recovery period without Cu-NP stress. Exposure to Cu-NPs significantly elevated antioxidant enzyme activities (GSH-Px, Cu/Zn-SOD) and thiobarbituric acid reactive substances (TBARS) level in liver and posterior kidney, indicating significant oxidative stress. In the liver, levels of epinephrine and diacylglycerol were significantly upregulated, the cAMP signaling pathway was disrupted, and the NF-κB signaling pathway was activated, along with the downregulation of ap-1 and erk1-2 and upregulation of gadd45β, reducing cell proliferation and viability. These alterations resulted in hepatocellular vacuolation and blurred outlines of hepatic lobules. In the gill, high-concentration Cu-NPs activated oxidative phosphorylation, phagosome, and cell-adhesion molecules pathways and downregulated genes related to cell proliferation, adhesion, and tight junctions (i.e., l1cam, camd1, cntn1, cdh2, and nectin1), leading to cellular vacuolization and epithelial separation in histology. These changes disrupted osmotic balance and significantly upregulated Na+/K+-ATPase activity. All histological damages were not fully recovered within the tested recovery period. Therefore, under conditions of continuous exposure, the concentration of Cu-NPs used for juvenile yellowtail kingfish in aquaculture should be kept below 0.120 mg/L, with a recovery period exceeding 7 days. These results reveal the toxicity mechanisms of Cu-NPs and provide a scientific basis for establishing safe application guidelines in yellowtail kingfish aquaculture.

Fishes doi: 10.3390/fishes11080476

Authors: Annalisa Cotugno Paolo Pastorino Lucio Fariano Sara Glorio Patrucco Fabio Bondavalli Giorgia Zicarelli Giulia Milanese Martina Alessandra Gini Giuseppe Esposito Cinzia Bergamino Pier Luigi Acutis Elena Bozzetta Marino Prearo Silvia Colussi

Proliferative kidney disease (PKD), caused by the myxozoan parasite Tetracapsuloides bryosalmonae, represents a major threat to salmonid populations and aquaculture, particularly under warming environmental conditions. In Italy, its distribution remains poorly documented. This study aimed to update the epidemiological status of PKD by investigating its occurrence in a trout farm (Piedmont, northwestern Italy), a previously unreported area. A total of 787 individuals of Oncorhynchus mykiss were sampled between May and October 2024 across three seasonal periods. Fish were examined using necropsy, bacteriological, and molecular analyses. Water temperature ranged from 12.4 to 20.3 °C, showing a clear seasonal trend. Overall PKD prevalence was 42.3%, with significant temporal variation, increasing from 23.0% in early summer to 73.0% in late summer, and declining to 3.9% in autumn. A multivariable logistic regression model showed that PKD-positive fish had a lower probability of presenting macroscopic lesions, while sampling period was the main predictor of infection. These results revealed a temporal mismatch between pathological and molecular findings, highlighting the need for further histopathological validation of the observed seasonal patterns. This study provides the first evidence of PKD in southwestern Piedmont, extending the currently documented distribution of the disease in Italy and highlighting the need for enhanced surveillance under climate change.

Fishes doi: 10.3390/fishes11080475

Authors: Jingyun Tian Liqiang Zhang Qihuan Zhang Yang Xu Xuan Wei Mingzhu Pan Zisheng Wang Zhitao Qi

Piscidins, fish-specific antimicrobial peptides (AMPs), play important roles in the innate immunity of fish against invading bacteria. In this study, a novel piscidin was identified in largemouth bass (Micropterus salmoides) (MSPiscidin-4), which contained an active peptide of 25 aa with an amphipathic helix possessing distinct hydrophobic and positively charged regions. MSPiscidin-4 belongs to the Group I piscidins as determined by sequence identity, homology modeling and phylogenetic tree analysis. MSPiscidin-4 was constitutively expressed in all seven selected tissues, with the highest transcript level in the gill and the lowest in the brain and spleen. Furthermore, MSPiscidin-4 was significantly up-regulated in spleen from 6 h to 24 h post-lipopolysaccharide (LPS) stimulation. A synthetic MSPiscidin-4 peptide was produced by the Fmoc solid-phase synthesis method and exhibited antibacterial activity against several aquatic bacterial strains, with the strongest against Aeromonas hydrophila, followed by Vibrio splendidus, Staphylococcus aureus, Edwardsiella tarda, and the weakest against E. coli and A. veronii. MSPiscidin-4 is the fourth piscidin reported in largemouth bass, showing distinct sequence identity (35.0–68.0% with previously reported MSPiscidins), physicochemical properties (net charge +5, pI 12.48), tissue distribution (highest expression in gill), and antibacterial potency (particularly strong against A. hydrophila). Our results enrich the piscidin components and deepen the understanding of piscidins against invading bacteria in largemouth bass.

Fishes doi: 10.3390/fishes11080474

Authors: Wenhao Sha Guiying Chen Bo Han Xinjun Chen Qilei Zhao

Recreational fisheries contribute significantly to global economies through tourism, employment, and ecosystem service valorization. However, a systematic understanding of their economic magnitude and regional disparities remains fragmented. This study conducts a systematic review of 112 peer-reviewed articles published between 1991 and 2024, synthesizing the economic evidence across three key domains: consumer behavior, resource management, and ecological interactions. Consistent with previous research, our systematic synthesis documents a pronounced imbalance in the existing evidence base: studies from high-income countries more frequently report established management frameworks (e.g., bag limits, catch-per-unit-effort monitoring) and robust economic valuation mechanisms (e.g., Willingness to Pay estimation), whereas low- and middle-income countries face significant barriers in infrastructure and resource quantification. We identify that non-market valuation methods, particularly the travel cost method and consumer surplus analysis, are critical for internalizing the environmental value of fisheries. Furthermore, while ecological restoration demonstrates clear positive feedback loops for local economies, the sector exhibits high vulnerability to external shocks, such as the COVID-19 pandemic. This review highlights the urgent need to bridge the data gap in developing regions and suggests that transferring successful adaptive management models from developed nations is essential for achieving equitable and sustainable growth in the global recreational fishery economy.

Fishes doi: 10.3390/fishes11080473

Authors: Deqin Luo Fanglian Lu Lian Yang Zhenbo Gan Xianbo Zhang Ranran Dong

Nonylphenol (NP), a typical emerging pollutant, is widely detected in water bodies, yet its hepatotoxic mechanisms and mitigation strategies remain underexplored. This study evaluated the protective effects of a mixed probiotic (Lactobacillus acidophilus and Bacillus subtilis) against NP-induced hepatotoxicity in Silurus meridionalis by integrating transcriptomic and metabolomic analyses, with validation by RT-qPCR and ELISA. The results showed that NP exposure disrupted the arachidonic acid (AA) pathway (activating pro-inflammatory COX and LOX pathways while the suppressing anti-inflammatory CYP450 branch), promoted ferroptosis via iron dyshomeostasis and oxidative damage, and impaired triglyceride (TG) synthesis. Probiotic pretreatment reversed these toxic effects by modulating AA metabolism, suppressing COX (ptgs2a↓ → PGE2↓) and LOX (alox12↓ → MDA↓) pathways, while upregulating the CYP450 pathway (cyp2j↑ → 11,12-EET↑). Probiotics also enhanced Fe3+ sequestration (steap4↑) and antioxidant defense (CAT↑, gpx4a↑), limiting Fenton reaction-mediated oxidative injury, and restored hepatic TG synthesis through upregulation of the DHAP-to-TG cascade (DHAP—(gpd1b↑) → G3P↑—(gpat3↑) → LPA—(agpat6↑) → PA—(plpp7↑) → DAG↑—(dgat2↑) → TG↑). These findings suggest that NP induces hepatotoxicity in S. meridionalis, involving ferroptosis, AA metabolism disruption and impaired TG synthesis as interconnected pathological events. Probiotics likely counteract this toxicity through systemic metabolic reprogramming. Collectively, these findings elucidate the hepatotoxic mechanisms of NP in S. meridionalis and offer toxicological data for its risk assessment, supporting the potential of probiotic-based strategies to mitigate emerging pollutant impacts in aquatic organisms.

Fishes doi: 10.3390/fishes11080472

Authors: Fumio Watanabe Kyohei Koseki Tomohiro Bito

In edible shellfish, vitamin B12 content has traditionally been evaluated based on total content; however, recent studies reveal substantial diversity in corrinoid composition among species. This review integrates molecular and ecological perspectives to reassess vitamin B12 levels in shellfish using cobamide fingerprinting. Filter-feeding bivalves generally exhibit vitamin B12-dominant profiles, whereas herbivorous gastropods often contain higher proportions of pseudovitamin B12, and carnivorous species display intermediate or vitamin B12-dominant patterns reflecting trophic transfer. In addition, physicochemical form and food processing influence vitamin B12 bioavailability. These findings collectively demonstrate that a precise nutritional assessment requires a comprehensive evaluation of both the total content and the molecular makeup of corrinoids.

Fishes doi: 10.3390/fishes11080471

Authors: Ivana Giovanna Zupičić Snježana Zrnčić Lea Vrbančić Donatella Volpatti Marco Galeotti Dražen Oraić Matea Alfier Dorotea Grbin

Tenacibaculosis, caused by Tenacibaculum maritimum, remains a major bacterial disease affecting marine aquaculture, particularly European seabass farming. This study evaluated the immune response and protective efficacy of a formalin-inactivated T. maritimum vaccine administered by immersion or intraperitoneal (i.p.) injection in European seabass (Dicentrarchus labrax). Each vaccination strategy was evaluated using its corresponding experimental challenge model 36 days post-vaccination. Vaccine performance was assessed by relative percentage of survival (RPS), expression of selected immune-related genes (IL-1β, IL-10, IgT), and specific serum IgM production. Intraperitoneal vaccination followed by i.p challenge provided significant protection, with 87% survival and an RPS of 67, accompanied by elevated serum IgM levels and pronounced systemic immune activation. Immersion-vaccinated fish also showed complete survival; however, the unexpectedly low mortality in the corresponding mock-vaccinated controls limited the discriminatory capacity of the immersion challenge model and prevented a robust assessment of vaccine efficacy according to the defined criteria. Gene expression analysis revealed distinct immune profiles, with immersion vaccination inducing an early but transient response, whereas i.p. vaccination elicited stronger and more sustained systemic activation, particularly within innate and humoral immune pathways. Principal component analysis further demonstrated clear clustering of immune responses according to vaccination route. These findings demonstrate the potential of an autogenous vaccine to protect European seabass against tenacibaculosis and highlight the importance of considering both vaccination route and the challenge model when interpreting vaccine efficacy. Further studies should optimise immersion vaccination protocols and investigate local mucosal immune responses to support the development of effective vaccination strategies for juvenile European seabass.