Fishes

13 pages, 1762 KB

Open AccessArticle

Preparation and Application of Monoclonal Antibodies Targeting IgM in Pearl Gentian Grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂)

by Xiaorui Qian, Jiong Wu, Jiamin Qiu, Yixin Li, Jialin Zhang, Xiaoli Xu, Yinan Wang and Qiang Li

Fishes 2026, 11(3), 160; https://doi.org/10.3390/fishes11030160 - 11 Mar 2026

Abstract

Viral and bacterial pathogen pathogens cause disease outbreaks that challenge the pearl gentian grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) industry’s sustainable development. The lack of monoclonal antibodies (mAbs) targeting serum immunoglobulin M (IgM) in this hybrid grouper impedes the development [...] Read more.

Viral and bacterial pathogen pathogens cause disease outbreaks that challenge the pearl gentian grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) industry’s sustainable development. The lack of monoclonal antibodies (mAbs) targeting serum immunoglobulin M (IgM) in this hybrid grouper impedes the development of non-lethal immunoassays for detecting pathogen infections, as well as research on immune responses following vaccination. We purified serum IgM from hybrid pearl gentian grouper and generated two mAbs—designated 41-H2-E1 and 62-E8-G9—against the purified IgM, finding that mAb 62-E8-G9 specifically recognized the IgM heavy chain, whereas mAb 41-H2-E1 specifically recognized the light chain. In indirect immunofluorescence assays, both mAbs reacted with surface Ig-positive (sIg⁺) lymphocytes. A double-antibody sandwich ELISA was subsequently established using mAb 62-E8-G9 as the capture antibody and HRP-conjugated mAb 41-H2-E1 as the detection antibody, enabling accurate quantification of serum IgM levels. Significant differences in IgM concentrations were observed between larger and smaller individuals (9.11 μg/mL vs. 3.84 μg/mL, p < 0.05). In immunostimulant administration experiments, both low-and high-dose groups exhibited approximately 2.0-fold higher IgM levels than the control group (p < 0.05). In contrast, vaccination with inactivated vaccines did not result in statistically significant differences in total IgM levels. mAb 41-H2-E1 was further applied to detect Vibrio parahaemolyticus- and Vibrio harveyi-specific immunoglobulins in serum under different vaccination regimens. Collectively, these findings demonstrated that the mAbs developed in this study served as reliable immunological tools for investigating immune function in hybrid pearl gentian grouper. Full article

(This article belongs to the Special Issue Advances in the Immunology of Aquatic Animals)

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16 pages, 1448 KB

Open AccessArticle

Microplastic Uptake in Fishes from Crișul Repede River (Bihor County, Romania): A Preliminary Study

by Diana Cupșa, Marcus Drimbea and Andrei Togor

Fishes 2026, 11(3), 159; https://doi.org/10.3390/fishes11030159 - 9 Mar 2026

Abstract

Microplastic (MP) pollution in freshwater is an important global issue affecting an increasing number of areas. MP is ingested by aquatic organisms and transferred through food chains, causing impacts on both aquatic life and human health. While studies on MP uptake in the [...] Read more.

Microplastic (MP) pollution in freshwater is an important global issue affecting an increasing number of areas. MP is ingested by aquatic organisms and transferred through food chains, causing impacts on both aquatic life and human health. While studies on MP uptake in the gastrointestinal tract (GIT) of fish are numerous globally, in Romania, there are extremely few. As a result, we conducted research on this phenomenon in fish species from the Crișul Repede River (CR) in two river sectors with different levels of anthropogenic impact. We found out that 100% of the collected fish had MPs in their GIT, with most of the particles being small-sized fragments (0.025–0.1 mm). Upstream, benthopelagic species ingested more MPs than downstream, whereas for benthic species, the amount of MPs in the GIT was greater downstream. Larger individuals contained more MPs than smaller ones. The presence of MPs in fish bodies can pose a problem if these particles enter internal organs and trigger adverse physiological effects. Full article

(This article belongs to the Special Issue Building a Sustainable Future for Inland Fisheries and Aquaculture in a Time of Multiple Stressors)

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13 pages, 1619 KB

Open AccessArticle

Acute Hypoxia Stress in the Mudskipper (Boleophthalmus pectinirostris): Effects of Puerarin and Dexamethasone

by Dexiang Feng, Qianqian Huang, Guangjun Wang, Xuyuan Shao and Zhifei Li

Fishes 2026, 11(3), 158; https://doi.org/10.3390/fishes11030158 - 9 Mar 2026

Abstract

The intensification of aquaculture often leads to dissolved oxygen depletion, posing a significant hypoxic stress to aquatic organisms such as the mudskipper (Boleophthalmus pectinirostris). Identifying compounds that can mitigate hypoxic damage is therefore of great importance. This study investigated the protective [...] Read more.

The intensification of aquaculture often leads to dissolved oxygen depletion, posing a significant hypoxic stress to aquatic organisms such as the mudskipper (Boleophthalmus pectinirostris). Identifying compounds that can mitigate hypoxic damage is therefore of great importance. This study investigated the protective effects of puerarin and dexamethasone against acute hypoxic stress in mudskippers. Four experiment groups were formulated: fish in the control group (HC) and the hypoxia group (HH) were injected with NaCl, fish in the puerarin group (HP) were injected with puerarin, and fish in the dexamethasone group (HD) were injected with dexamethasone, then the HH, HP, and HD groups were treated with a hypoxia condition sustained for 48 h. Compared with the HC and HP groups, the HH group showed significantly reduced activities of protein kinase B (Akt), glycogen synthase kinase (GSK-3β), lactate dehydrogenase (LDH), and pyruvate kinase (PK) in the liver at 24 and 48 h. The gene transcription levels of GSK-3β and Akt in the liver and gill of mudskipper were the smallest, but p53, VEGF, HIF-1, and BNIP3 in the liver of fish in the HH group were significantly highest. The gene transcription levels of GSK-3β and Akt in the liver of mudskippers in the HP group were observably lower than those of mudskippers in the HD group at 24 h, but HIF-1 was significantly higher. On the contrary, at 48 h, the mRNA expression levels of GSK-3β and Akt in the liver of fish in the HP group were significantly higher than those of fish in the HD group, but HIF-1 was significantly lower. The results indicated that mudskippers suffering from hypoxia led to oxygen homeostasis disturbances and apoptosis, but exogenous puerarin or dexamethasone could mitigate the adverse effects. The mRNA of HIF-1 regulation has an important role in enhancing hypoxia tolerance. Full article

(This article belongs to the Special Issue Fish Nutrition and Immunology)

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20 pages, 3115 KB

Open AccessArticle

Diversity and Distribution of the Order Tetraodontiformes in Spain: New Records, Biological Insights and Ecological Implications

by Rafael Bañón, Bruno Almón, Begoña Ben-Gigirey, Andrés Villaverde, Mónica González-Castrillón, Rosario Domínguez-Petit, Carlos García Soler and Alejandro de Carlos

Fishes 2026, 11(3), 157; https://doi.org/10.3390/fishes11030157 - 9 Mar 2026

Abstract

This study documents the presence of two uncommon tetraodontiform fishes and reviews the occurrence of species from this order in Spanish marine waters. Two tetraodontid specimens (Family Tetraodontidae) were caught in the Atlantic waters off the coast of Galicia, northwestern Spain. A specimen [...] Read more.

This study documents the presence of two uncommon tetraodontiform fishes and reviews the occurrence of species from this order in Spanish marine waters. Two tetraodontid specimens (Family Tetraodontidae) were caught in the Atlantic waters off the coast of Galicia, northwestern Spain. A specimen of Sphoeroides pachygaster was collected in 2021 off the Costa da Vela, while a specimen of Ephippion guttifer was captured in 2025 in the Ría de Pontevedra, both locations situated in southern Galicia. Morphological analyses, supported by photographic evidence and DNA barcoding, confirmed the preliminary taxonomic identification of the two species. Histological reproductive analysis of the Ephippion guttifer specimen revealed a female in the spawning-capable phase. These findings constitute the first verified record of S. pachygaster and the second of E. guttifer in Galician waters. An updated comprehensive list of tetraodontiform species found in Spanish waters across five geographical demarcations was compiled. Historically, a total of 26 species across five families have been reported in Spanish waters, with 22 in the Canary Islands and 15 in the Spanish Iberian Peninsula and Balearic Islands. Additionally, a review of the presence of neurotoxic tetrodotoxins (TTXs) or paralytic shellfish toxins (PSTs) in each species is included, providing an up-to-date overview of a largely unexplored field in European waters. The increasing occurrence of tetraodontiform fishes in Spanish waters provides further evidence of the progressive tropicalization of the Spanish marine environment. Full article

(This article belongs to the Section Taxonomy, Evolution, and Biogeography)

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20 pages, 12018 KB

Open AccessArticle

Physiological Benefits of Probiotic Refeeding After Short-Term Fasting in Nile Tilapia: Growth Performance, Histomorphological, and Gene Expression Responses

by Mohsen A. Khormi, Walaa F. A. Emeish, Mahmoud Nasr, Fatma A. Madkour and Karima A. Bakry

Fishes 2026, 11(3), 156; https://doi.org/10.3390/fishes11030156 - 8 Mar 2026

Abstract

This study investigated the physiological benefits of probiotic supplementation during refeeding after short-term fasting in Nile tilapia (Oreochromis niloticus). A total of 180 fish were assigned to three groups: continuously fed control or subjected to 5 days of fasting followed by [...] Read more.

This study investigated the physiological benefits of probiotic supplementation during refeeding after short-term fasting in Nile tilapia (Oreochromis niloticus). A total of 180 fish were assigned to three groups: continuously fed control or subjected to 5 days of fasting followed by 15 days of refeeding with either a basal or probiotic-enriched diet containing Bacillus subtilis, B. licheniformis, and B. pumilus. Growth performance indices (body weight, length, weight gain, specific growth rate, condition factor, relative feed intake, and feed conversion ratio) were measured. Muscle samples were collected for histomorphological evaluation and quantitative real-time PCR analysis of antioxidant genes catalase (cat) and superoxide dismutase 2 (sod-2), growth-related genes insulin-like growth factor 1 (igf-1) and suppressor of cytokine signaling 2 (soc-2), anti-inflammatory gene transforming growth factor beta (tgf-β), and myostatin genes. Fasting significantly reduced (p < 0.05) body weight compared to control, confirming the impact of nutrient deprivation. Upon refeeding, fish on the basal diet showed partial growth recovery but remained below control levels, whereas probiotic-fed fish exhibited superior recovery, surpassing both control and basal groups in body weight, length and weight gain. Condition factor exhibited insignificant changes among all groups after fasting and upon refeeding. Specific growth rate of the entire experiment was highest in the probiotic group, while insignificant. Relative feed intake decreased in both refed groups, yet feed conversion ratio improved, particularly with probiotics. Gene expression analysis revealed fasting-induced upregulation of antioxidant (cat and sod-2) and myostatin (p < 0.05), alongside downregulation of growth-related (igf-1 and soc-2) and anti-inflammatory (tgf-β) genes (p < 0.05). Basal refeeding restored most expressions, whereas probiotics enhanced antioxidant, growth, and anti-inflammatory genes while normalizing myostatin (p > 0.05 vs. control). Histological evaluation showed fasting-induced muscle atrophy, which was most effectively reversed by probiotics. Overall, probiotics accelerated recovery, highlighting their potential to optimize post-fasting growth in aquaculture. Full article

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

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23 pages, 1230 KB

Open AccessArticle

Synergistic Effects of Multiple Non-Native Species and Phenotypic Plasticity Facilitate the Establishment of Yellow Catfish (Pelteobagrus fulvidraco) in Lake Erhai, a Subtropical Plateau Lake: Trophic Expansion and Robust Body Condition

by Chuanyan Zhong, Zhuanxing Shao, Weile Chu, Jimeng Feng, Jian Shen, Xinze Wang and Xiaowen Long

Fishes 2026, 11(3), 155; https://doi.org/10.3390/fishes11030155 - 8 Mar 2026

Abstract

The successful establishment of non-native fish often relies on life-history plasticity and opportunistic trophic strategies. This study elucidates the invasion mechanisms of the non-native yellow catfish (Pelteobagrus fulvidraco) in Lake Erhai, a plateau lake in China, by integrating morphometrics, stable isotope [...] Read more.

The successful establishment of non-native fish often relies on life-history plasticity and opportunistic trophic strategies. This study elucidates the invasion mechanisms of the non-native yellow catfish (Pelteobagrus fulvidraco) in Lake Erhai, a plateau lake in China, by integrating morphometrics, stable isotope analysis, and DNA metabarcoding. Our results reveal a “triple mechanism” driving this invasion success. First, the population exhibits significant phenotypic plasticity, manifesting as enhanced somatic growth and superior body condition (mean condition factor: 1.92) and sexually dimorphic growth favoring males. Second, DNA metabarcoding confirms a broad trophic niche dominated by zooplankton (31.70%) and, critically, other non-native fishes (Hypomesus nipponensis and Neosalanx taihuensis), providing strong empirical support for the synergistic effects of multiple non-native species. This predation on high-energy forage fish likely fuels the observed somatic growth and high reproductive output, counteracting the typical size-reduction trade-offs often seen in biological invasions. Third, reproductive assessment indicates a protracted spawning period (spanning at least from spring through summer) and an absolute fecundity (mean: 8471 ± 2194 eggs) consistent with its strategy of producing larger, high-quality eggs, significantly exceeding that of native riverine populations. These findings suggest that P. fulvidraco effectively exploits altered food webs—specifically pre-existing invasive prey—to maximize somatic growth and reproductive output, thereby establishing dominance in the plateau lake ecosystem. Therefore, effective management strategies must go beyond single-species control and prioritize controlling pre-existing invasive forage fish to disrupt the facilitation pathway driven by ecosystem alteration by invasive species. Full article

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

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14 pages, 4923 KB

Open AccessArticle

Within-Reef and Within-Creek Relatedness Contributes to Fine-Scale Population Structure in Oysters Along the Georgia Coast

by J. Scott Harrison, Sarah Batchelor, Jessica C. Watts and John M. Carroll

Fishes 2026, 11(3), 154; https://doi.org/10.3390/fishes11030154 - 7 Mar 2026

Abstract

Marine species with high fecundity and larvae with long-distance dispersal potential can have complex population genetic patterns. Characterizing population structure in these species is important for understanding their ecology and life history and designing management strategies. The eastern oyster (Crassostrea virginica) [...] Read more.

Marine species with high fecundity and larvae with long-distance dispersal potential can have complex population genetic patterns. Characterizing population structure in these species is important for understanding their ecology and life history and designing management strategies. The eastern oyster (Crassostrea virginica) is both ecologically and economically important but has experienced recent population declines. Characterizing genetic variation in regional C. virginica populations will contribute to conservation and restoration practices. We used 20 nuclear microsatellite loci to examine genetic diversity, population structure, and kinship within and among wild oyster populations in coastal Georgia. Oysters were sampled from multiple fringe reefs within a single tidal creek and from four estuarine creeks spanning approximately 115 km of coastline. Genetic diversity was high across all sites, but modest yet significant population structure was detected at both local and regional scales. Within a single creek, significant genetic differentiation was observed among reefs separated by only a few kilometers. Kinship analyses revealed significantly higher relatedness within reefs and within creeks than among locations relative to random expectations. These results indicate that regional coastal dynamics, kin aggregation, local retention, and sweepstakes reproductive success contribute to fine-scale genetic structure despite high dispersal potential. Our findings suggest that accounting for local retention is important when designing oyster restoration, broodstock selection, and management strategies in dynamic estuarine and coastal environments. Full article

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

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20 pages, 1009 KB

Open AccessArticle

Low-Carbon Certification vs. Carbon Surcharges: A Recursive Dynamic GTAP Assessment of EU/UK Border Measures for China’s Seafood Exports

by Xianrui Mo and Zefang Liao

Fishes 2026, 11(3), 153; https://doi.org/10.3390/fishes11030153 - 6 Mar 2026

Abstract

This study compares two policy instruments for decarbonizing China’s seafood exports to the EU and UK over 10 years using a recursive dynamic computable general equilibrium model. One instrument applies tariff-like carbon surcharges on embedded emissions at the border. The other recognises certified [...] Read more.

This study compares two policy instruments for decarbonizing China’s seafood exports to the EU and UK over 10 years using a recursive dynamic computable general equilibrium model. One instrument applies tariff-like carbon surcharges on embedded emissions at the border. The other recognises certified low-carbon production through tiered rate reductions or exemptions. The model constructs product-level carbon cost wedges for processing electricity, aluminium packaging, and cold-chain operations, then transmits them to border prices through pass-through and to import volumes through Armington demand. These mechanisms operate inside a dynamic setting with capital accumulation, learning, and technology adoption. We evaluate processed tuna, shrimp, whitefish, and fresh tilapia to reflect differences in energy use, packaging intensity, and cold-chain reliance. Results show that certification, especially when paired with targeted domestic green finance or tax offsets, speeds adoption of cleaner power and refrigerants and preserves market share better than uniform surcharges. Effects differ between coastal and inland production hubs, supporting location-specific policy bundles. Sensitivity analysis varies carbon prices, adoption speeds, and certification coverage within stated parameter ranges. We report trade, export revenue, emissions, investment, and welfare outcomes and identify product and channel drivers of exposure. Full article

(This article belongs to the Section Fishery Economics, Policy, and Management)

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18 pages, 1276 KB

Open AccessArticle

Dietary Replacement of Fish Oil with Plant Oils and Schizochytrium limacinum Biomass Modulates Gut Microbiota Composition and Functional Potential in European Sea Bass (Dicentrarchus labrax)

by Federico Moroni, Simona Rimoldi, Antonia Bruno, Giulia Agostinetto, Violeta Kalemi, Valerio Mezzasalma and Genciana Terova

Fishes 2026, 11(3), 152; https://doi.org/10.3390/fishes11030152 - 6 Mar 2026

Abstract

Aquaculture sustainability requires a reduction in the reliance on marine-derived raw materials such as fish oil in aquafeeds while maintaining fish health and product quality. This study investigated the effects of replacing fish oil with plant oils supplemented with DHA-rich Schizochytrium limacinum biomass [...] Read more.

Aquaculture sustainability requires a reduction in the reliance on marine-derived raw materials such as fish oil in aquafeeds while maintaining fish health and product quality. This study investigated the effects of replacing fish oil with plant oils supplemented with DHA-rich Schizochytrium limacinum biomass on the gut microbiota of European sea bass (Dicentrarchus labrax). S. limacinum SR21—an oleaginous microalga naturally rich in omega-3 fatty acids—was produced through heterotrophic fermentation using crude glycerol, a waste stream from biodiesel production, within a circular economy framework. A 21-week feeding trial was conducted in an indoor recirculating aquaculture system using 280 fish distributed across eight tanks. Four experimental diets were tested: fish oil-based (FO), plant oil-based without microalga (VO + 0), and plant oil-based supplemented with 5% (VO + 5) or 10% (VO + 10) microalgal biomass. Gut microbiota was analyzed in 22 fish per group using 16S rRNA gene sequencing. While alpha and beta diversity analyses of gut microbiota revealed modest structural shifts at phylum and class ranks, genus-rank differences were evident, with Lactobacillus and Clostridium sensu stricto associated with FO and VO + 0 diets, and Pseudomonas and Staphylococcus enriched in microalga-supplemented groups. Functional inference highlighted enhanced bile acid biosynthesis and carbohydrate metabolism in VO + 0, whereas antioxidant-related pathways, including ubiquinone and carotenoid biosynthesis, were stimulated in VO + 5 and VO + 10 groups. These results demonstrate that S. limacinum biomass modulates microbiota functional capacity, potentially contributing to oxidative stress mitigation and host resilience. The findings support microbiota-informed feed formulation strategies to advance sustainable aquaculture. Full article

(This article belongs to the Section Nutrition and Feeding)

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19 pages, 907 KB

Open AccessArticle

Comparative Effects of Untreated and High-Solid Loading Pre-Treated Codium tomentosum on Oxidative and Immune Responses in European Seabass (Dicentrarchus labrax)

by Catarina Ramos-Oliveira, Rui Magalhães, Cláudia Serra, Isabel Belo, Aires Oliva-Teles and Helena Peres

Fishes 2026, 11(3), 151; https://doi.org/10.3390/fishes11030151 - 6 Mar 2026

Abstract

The effects of dietary inclusion of the macroalgae Codium tomentosum, either untreated or pre-treated with high-solid-loading alkaline hydrolysis, on the oxidative status, intestinal immune responses, and gut microbiota was evaluated in European seabass juveniles. Four diets, a control diet (CTR) and three [...] Read more.

The effects of dietary inclusion of the macroalgae Codium tomentosum, either untreated or pre-treated with high-solid-loading alkaline hydrolysis, on the oxidative status, intestinal immune responses, and gut microbiota was evaluated in European seabass juveniles. Four diets, a control diet (CTR) and three diets containing 7.5% C. tomentosum, either untreated (COD) or pre-treated for 30 min (COD30) or 60 min (COD60), were formulated and fed for 11 weeks. Fish fed the COD30 diet showed increased intestinal lipid peroxidation, higher plasma lysozyme activity, and reduced total glutathione, compared with CTR and COD. In parallel, distal intestine inflammatory (TNF-α, IL-10, IL-1β) and apoptotic (CASP3, CASP9) gene expression was downregulated relative to COD diet, suggesting a dissociation between oxidative damage and inflammatory activation. In fish fed COD60, intestinal lipid peroxidation plasma lysozyme activity were reduced and distal intestine inflammatory and apoptotic gene expression was lower than in COD diet. Hepatic oxidative stress markers were not affected by dietary treatment. DGGE analysis revealed no significant changes in microbial richness or diversity, although COD30 increased digesta community similarity. Overall, high-solid-loading alkaline pre-treatment of C. tomentosum for 60 min mitigated the oxidative and inflammatory/apoptotic impacts associated with dietary inclusion of the untreated macroalga, supporting ingredient processing as a strategy to improve the functional value of macroalgal aquafeeds. Full article

(This article belongs to the Special Issue Pivotal Roles of Feed Additives for Fish)

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22 pages, 661 KB

Open AccessArticle

Operational Performance of Aquavoltaics Under Different Stakeholder Cooperation Schemes: Evidence from White Shrimp Aquaculture in Taiwan

by Bo-Ying Chen, Po-Lin Huang, Yen-Lung Hou, Farok Afero, Szu-Han Liu and Cheng-Ting Huang

Fishes 2026, 11(3), 150; https://doi.org/10.3390/fishes11030150 - 6 Mar 2026

Abstract

Aquaculture faces rising climate-change risks, while photovoltaic power generation requires substantial land resources, underscoring the need for multifunctional land use in the energy transition. Aquavoltaics—combining aquaculture with solar power—has emerged, and its success depends on stakeholder cooperation. Using white shrimp aquaculture in Taiwan [...] Read more.

Aquaculture faces rising climate-change risks, while photovoltaic power generation requires substantial land resources, underscoring the need for multifunctional land use in the energy transition. Aquavoltaics—combining aquaculture with solar power—has emerged, and its success depends on stakeholder cooperation. Using white shrimp aquaculture in Taiwan as a case study, this study examines four cooperation schemes—a sole-investment scheme, a photovoltaic-led leasing scheme, a landowner lease-back scheme, and a separated aquaculture and photovoltaic operation scheme—across six aquavoltaic types. Cost–benefit and data envelopment analyses assess the economic returns and operational efficiency of aquaculture operators and photovoltaic companies under each scheme. The results show that all schemes offer profit potential but differ in efficiency and income distribution. The landowner lease-back scheme is most efficient for aquaculture operators, while photovoltaic companies operate near the efficiency frontier in all schemes. The findings highlight that cooperation design shapes the economic feasibility, efficiency, and livelihood impact of aquavoltaic systems, providing a useful reference for future policy and model design. Full article

(This article belongs to the Special Issue Building a Sustainable Future for Inland Fisheries and Aquaculture in a Time of Multiple Stressors)

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16 pages, 1524 KB

Open AccessArticle

Feasibility of a Close-Kin Mark-Recapture for Stock Assessment of Indian Ocean Swordfish (Xiphias gladius)

by Thomas Chevrier, Dominique A. Cowart, Anne-Elise Nieblas, Jérémie Chanut, Serge Bernard and Sylvain Bonhommeau

Fishes 2026, 11(3), 149; https://doi.org/10.3390/fishes11030149 - 4 Mar 2026

Abstract

The Indian Ocean Tuna Commission (IOTC) manages swordfish, Xiphias gladius, a species of high economic importance in the Indian Ocean. Current stock assessments rely on catch per unit effort indices, which can be biased, complicating reliable abundance estimates. We explored alternative approaches [...] Read more.

The Indian Ocean Tuna Commission (IOTC) manages swordfish, Xiphias gladius, a species of high economic importance in the Indian Ocean. Current stock assessments rely on catch per unit effort indices, which can be biased, complicating reliable abundance estimates. We explored alternative approaches by assessing the feasibility of the close-kin mark– recapture (CKMR) method, a powerful genetic-based approach. This pilot study aimed to validate protocols and guide future CKMR implementation at the IOTC scale. CKMR simulations were conducted to estimate the sample sizes required to detect sufficient kin pairs. Kinship analyses assumed a single panmictic population across the Indian Ocean, consistent with current IOTC management. A total of 2068 individuals were genotyped using SNP markers, identifying one parent-offspring pair (POP) and at least two half-sibling pairs (HSPs). As predicted by simulations, this sampling scale precludes robust estimation. However, results indicate that robust CKMR-based estimates could be achieved by sampling at least 18,000 swordfish over three years, representing about 20% of the current sampling effort already undertaken by contracting parties. The annual cost of genomic data generation for CKMR represents less than 0.5% of the first-sale market of swordfish in the Indian Ocean. Overall, this study supports the feasibility of CKMR for swordfish and provides a foundation for scaling up future programs to improve Indian Ocean stock assessments. Full article

(This article belongs to the Section Biology and Ecology)

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20 pages, 5608 KB

Open AccessArticle

In Situ Cultivation of Autotrophic Bioflocs Enables Zero-Water-Exchange Intensive Shrimp Farming: Mechanisms and Applications

by Miao Xie, Yongkui Liu, Xuanzhi Hu, Miao Zhang, Huanying Pang, Jia Cai, Yishan Lu, Jichang Jian and Yu Huang

Fishes 2026, 11(3), 148; https://doi.org/10.3390/fishes11030148 - 2 Mar 2026

Abstract

Research on heterotrophic bioflocs is extensive, whereas investigations into autotrophic bioflocs remain limited. This study established an in situ autotrophic biofloc (ABF) system for intensive Pacific white shrimp (Penaeus vannamei) farming, aiming for zero water exchange and optimized water quality. A [...] Read more.

Research on heterotrophic bioflocs is extensive, whereas investigations into autotrophic bioflocs remain limited. This study established an in situ autotrophic biofloc (ABF) system for intensive Pacific white shrimp (Penaeus vannamei) farming, aiming for zero water exchange and optimized water quality. A 120-day indoor experiment tested three stocking densities (300 (T1), 250 (T2), and 200 shrimp per m³ (T3)) with no water exchange. Water quality was monitored every two days, and bacterial communities were analyzed on days 10 and 70. The results indicated that ABF maturation was achieved by day 70 across all treatments, marked by three key indicators: (1) synchronous declines in nitrite and nitrate concentrations; (2) concurrent decreases in pH and total alkalinity approaching maturation; and (3) sustained high nitrogen removal efficiency (nitrite < 0.7 mg/L, ammonia < 0.6 mg/L). All density groups displayed similar patterns in both water quality dynamics and microbial community evolution. Bacterial analysis revealed that dominant genera such as Ruegeria, Bacillus, Muricauda, SM1A02, and Nitrospira played critical roles in toxic nitrogen removal, while pathogenic Klebsiella and Vibrio significantly decreased post-maturation. Heterotrophic nitrification and aerobic denitrification microorganisms (HNADMs) were identified as potentially responsible for nitrite accumulation. Nitrite accumulation was found in all groups. T2 and T3 achieved satisfactory breeding performance despite pre-maturation nitrate peaks exceeding 40 mg/L, whereas T1 suffered a low survival rate (27.47%) due to severe nitrite accumulation (>50 mg/L). A biofloc volume (BFV) of 4–8 mL/L effectively managed daily feed inputs of 75–110 g/m³. These findings lay a theoretical and technical foundation for the application of in situ ABF cultivation in intensive farming and enhance the sustainability of aquaculture. Full article

(This article belongs to the Special Issue An Issue in Honor of Yoram Avnimelech: Application of Biofloc Technology (BFT))

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21 pages, 2150 KB

Open AccessArticle

The Relationship Between Respiration Rates and Electron Transport System Activity in Fish

by Ione Medina-Suárez and Santiago Hernández-León

Fishes 2026, 11(3), 147; https://doi.org/10.3390/fishes11030147 - 2 Mar 2026

Abstract

Fishes contribute to the biological carbon pump, yet their overall role remains poorly constrained due to the difficulty of obtaining direct metabolic measurements and, consequently, is poorly understood. Electron transport system (ETS) activity is commonly used as a proxy for potential respiration, but [...] Read more.

Fishes contribute to the biological carbon pump, yet their overall role remains poorly constrained due to the difficulty of obtaining direct metabolic measurements and, consequently, is poorly understood. Electron transport system (ETS) activity is commonly used as a proxy for potential respiration, but its application requires an appropriate relationship between respiration (R, measured as oxygen consumption MO₂) and ETS activity. Here, we examined the relationship between swimming activity, oxygen consumption, and ETS activity in juvenile Sparus aurata using swimming-tunnel respirometry. Oxygen consumption increased with swimming speed following a four-parameter sigmoidal model, whereas ETS activity remained independent of short-term changes in activity. Normalizing respiration by ETS produced R/ETS ratios ranging from 0.17 to 0.71, values consistent with those reported for zooplankton and micronekton. Lower ratios correspond to minimal aerobic demand and may represent quiescent behaviour, while higher ratios reflect elevated demands associated with active movement or feeding. These ratios are suggested for the assessment of respiration rates from ETS activity during diel vertical migration in the ocean to improve estimates of respiratory flux. However, methodological issues related to ETS activity in different body regions must be solved to enable reliable measurements. Full article

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

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13 pages, 3174 KB

Open AccessArticle

A Case Study of Coilia nasus: Is There a Difference in Microchemical Signatures Between Left and Right Fish Sagittae?

by Chengchao Du, Tao Jiang and Jian Yang

Fishes 2026, 11(3), 146; https://doi.org/10.3390/fishes11030146 - 2 Mar 2026

Abstract

Owing to the asynchronous deposition of trace elements between paired left and right otoliths within individual fish, researchers must consciously and uniformly use only single otoliths (especially the left one) for microchemical studies. To ensure reliability of unilateral otolith data for inferring the [...] Read more.

Owing to the asynchronous deposition of trace elements between paired left and right otoliths within individual fish, researchers must consciously and uniformly use only single otoliths (especially the left one) for microchemical studies. To ensure reliability of unilateral otolith data for inferring the same habitat experiences of individual fish, this study focused on Coilia nasus as a representative case to validate whether the microchemical composition was consistent between left and right sagittal otoliths. Electron probe microanalysis was employed to determine microchemical profiles of Sr and Ca in both otoliths of 20 wild C. nasus specimens of the same age. At the individual level, Sr/Ca ratios in corresponding micro-regions (e.g., core and edge) of bilateral otoliths showed highly significant positive correlations, with approximately 92.59% of paired comparisons showing no significant differences at equivalent life-history stages, demonstrating that microchemical signals recorded by either otolith are highly consistent in both spatial distribution and elemental concentration levels. This study provides evidence of fundamental concordance in microchemical composition between bilateral otoliths within an individual, providing critical references on the methodological foundation for reliably using either the left or right otolith in future studies on otolith microchemistry of fish population connectivity, migration characteristics, and life history reconstruction. Full article

(This article belongs to the Special Issue Application of Otoliths in Fish Ecology and Fisheries)

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19 pages, 2775 KB

Open AccessArticle

Resource Characteristics of Six Rare and Endemic Fish Species in the Dam-Regulated Hongshui River and Their Relationships with Environmental Factors

by Yizhu Chen, Jiayang He, Li Wang, Zhihui Liu, Zhiqiang Wu, Yangyan Sun and Yusen Li

Fishes 2026, 11(3), 145; https://doi.org/10.3390/fishes11030145 - 28 Feb 2026

Abstract

To assess the impacts of cascade dam development on riverine fish, this study investigated the population structure and spatiotemporal distribution of six rare and endemic fish species in the Hongshui River mainstream from 2022 to 2023. Results indicated a significant resource decline, with [...] Read more.

To assess the impacts of cascade dam development on riverine fish, this study investigated the population structure and spatiotemporal distribution of six rare and endemic fish species in the Hongshui River mainstream from 2022 to 2023. Results indicated a significant resource decline, with the proportion of rare species dropping to 18.33%. Populations exhibited pronounced characteristics of age rejuvenation and miniaturization, with mean body lengths failing to reach growth inflection points. Although growth parameter analysis indicated rapid growth patterns (k > 0.2), stock assessment revealed that Semilabeo obscurus and Onychostoma gerlachi were overexploited (E > E_max), while Ptychidio jordani maintained the highest biomass. Redundancy analysis (RDA) identified water chemistry (e.g., conductivity, TN) as the primary driver of seasonal distribution, whereas the proportion of natural free-flowing river segments significantly influenced community variation under dam regulation (corresponding 59.44% of variation). Conservation strategies should prioritize the protection of remnant natural river segments, implementation of ecological flow regulation to simulate natural hydrological rhythms, and strict enforcement of minimum capture size limits to ensure the sustainable utilization of these rare and endemic resources. Full article

(This article belongs to the Special Issue Biodiversity and Spatial Distribution of Fishes, Second Edition)

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19 pages, 2151 KB

Open AccessArticle

The Feeding Habits and Length–Weight Relationships of the Invasive Black Bullhead Ameiurus melas (Rafinesque, 1820) in the Gruža Reservoir, Central Serbia

by Milena Radenković, Nataša Kojadinović, Aleksandra Milošković, Tijana Veličković, Milica Stojković Piperac, Aleksa Cvetković and Vladica Simić

Fishes 2026, 11(3), 144; https://doi.org/10.3390/fishes11030144 - 27 Feb 2026

Abstract

Invasive freshwater fishes often display high trophic plasticity, facilitating their establishment and persistence in novel environments. This study examined the feeding ecology, growth patterns, and trophic role of the invasive black bullhead Ameiurus melas in the eutrophic Gruža Reservoir (Central Serbia), with emphasis [...] Read more.

Invasive freshwater fishes often display high trophic plasticity, facilitating their establishment and persistence in novel environments. This study examined the feeding ecology, growth patterns, and trophic role of the invasive black bullhead Ameiurus melas in the eutrophic Gruža Reservoir (Central Serbia), with emphasis on ontogenetic dietary shifts and potential ecological impact. Diet composition was analyzed in 103 individuals representing three age classes using traditional diet indices, Costello graphical analysis, self-organizing maps (SOMs), and the Indicator Value (IndVal). Chironomidae, Protozoa, and fish eggs were the dominant dietary components across age classes, although their relative importance varied ontogenetically. Younger individuals exhibited a more generalized feeding strategy, whereas older fish showed increased specialization on benthic prey. SOM-IndVal analyses revealed prey taxa associated with specific feeding patterns at the individual level, identifying Diptera as an indicator prey not detected by population-level indices. Length–weight relationships indicated negative allometric growth (b < 3) across all age classes, consistent with a diet dominated by low-energy prey. These feeding patterns may contribute to altered benthic processes, reduced native fish recruitment, and reinforcement of eutrophic conditions. Overall, the results highlight the pronounced trophic flexibility and ecological plasticity of A. melas, supporting its invasive success in degraded freshwater ecosystems. Full article

(This article belongs to the Special Issue Trophic Ecology of Freshwater and Marine Fish Species)

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21 pages, 2720 KB

Open AccessArticle

Variation in Biofilm Formation of Bacteria Isolated from Fish Catch and Surfaces of a Fishing Vessel

by Natalija Topić Popović, Krunoslav Bojanić, Maro Bujak, Snježana P. Kazazić, Giorgia Bignami, Branka Bilić, Rozelindra Čož-Rakovac and Ivančica Strunjak-Perović

Fishes 2026, 11(3), 143; https://doi.org/10.3390/fishes11030143 - 27 Feb 2026

Abstract

This pioneering study investigates bacteria isolated from marine pelagic fish, fishing vessels, and gear surfaces, focusing on the variability in biofilm formation across different substrates, media, and cultivation conditions. Bacteria from fish intestines, skin, and gills, including spoilage organisms and potential fish and [...] Read more.

This pioneering study investigates bacteria isolated from marine pelagic fish, fishing vessels, and gear surfaces, focusing on the variability in biofilm formation across different substrates, media, and cultivation conditions. Bacteria from fish intestines, skin, and gills, including spoilage organisms and potential fish and human pathogens, can contaminate vessel surfaces, gear, and containers and may act as microbial reservoirs and transmission vectors. In this study, biofilm formation was evaluated at air–liquid interfaces and on submerged plastic, metal, and glass surfaces under various incubation temperatures and media. Vibrio spp. were isolated both from fishing nets and fish gills, particularly Vibrio alginolyticus, V. gigantis, and V. pelagius. Although V. harveyi was examined as a representative vibrio, it did not form a biofilm on polypropylene. Photobacterium damselae subsp. damselae, Pseudomonas fragi, P. gessardii, Psychrobacter spp., and Rothia endophytica showed a strong affinity for stainless steel. Overall adhesion regardless of media type was highest for P. gessardii, followed by P. damselae and Aeromonas veronii, which adhered strongly to steel, glass, and polypropylene; however, only P. gessardii also adhered well to polystyrene, an important finding because these are known fish and human pathogens. These results highlight species-dependent biofilm triggers and their substantial variability and provide guidance for standardized marine biofilm protocols. Full article

(This article belongs to the Special Issue The Impact of Contamination on Fishes)

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17 pages, 4382 KB

Open AccessArticle

Modulation of Different Salinity Conditions on Transcriptional Signature of Metabotropic Serotonin and Dopamine Receptors in Nile Tilapia (Oreochromis niloticus)

by Ming-Yuan Wu, Pichayapa Meekuan, Zhuo-Hang Feng, Zheng-Xiang Zhang, Ya-Xin Wang, Yue-Yan Sun, Zhi-Shuai Hou and Zhen-Fa Qin

Fishes 2026, 11(3), 142; https://doi.org/10.3390/fishes11030142 - 27 Feb 2026

Abstract

As freshwater resources become increasingly limited, exploiting brackish and marine waters for aquaculture is viewed as a promising alternative. Nile tilapia (Oreochromis niloticus), although considered euryhaline, shows relatively restricted tolerance to salinity compared with other tilapia species, making it an ideal [...] Read more.

As freshwater resources become increasingly limited, exploiting brackish and marine waters for aquaculture is viewed as a promising alternative. Nile tilapia (Oreochromis niloticus), although considered euryhaline, shows relatively restricted tolerance to salinity compared with other tilapia species, making it an ideal model to study adaptive responses to osmotic stress. Serotonin (5-HT) and dopamine (DA) are key modulators of stress responses through their activation of metabotropic G protein-coupled receptors (GPCRs). In this study, we investigated the transcriptional profiles of metabotropic serotonin and dopamine receptors across the brain, intestine, and liver of Nile tilapia reared in different salinity conditions (0 ppt, 16 ppt, 30 ppt). The results showed both dopamine and serotonin metabotropic receptors were duplicated with potential neofunctionalization, contributing to osmoregulatory capacity. Nile tilapia showed altered brain drd1, htr1 and htr7 subtypes in response to salt change. Meanwhile, the drd3 subtype showed pronounced alterations in the intestine and liver under elevated salinity. Notable transcriptional alterations in htr4 subtypes were observed in both brain and liver, suggesting their potential involvement in modulating energy balance and stress adaptation. Correlation network analyses further demonstrated coordinated regulation among receptor paralogues in the brain. These findings provide potential targets, such as ligand analog additives or genetic enhancement, for future functional validation and for improving salinity tolerance in Nile tilapia culture. Full article

(This article belongs to the Special Issue Physiological and Behavioral Studies in Aquaculture)

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