Fishes

21 pages, 2346 KB

Open AccessArticle

Genetic Analysis of Mixed Individuals Reveals Different Spawning Populations of the Tetrapturus pfluegeri (Longbill Spearfish) in the Western Atlantic Ocean

by Suhaila Karim Khalil Jaser, Caio Augusto Perazza, Rodrigo Rodrigues Domingues, Freddy Arocha, Eric Hallerman and Alexandre Wagner Silva Hilsdorf

Fishes 2026, 11(4), 253; https://doi.org/10.3390/fishes11040253 - 21 Apr 2026

Viewed by 376

Abstract

Populations of several billfish species are declining due to overfishing and bycatch, and fundamental aspects of their biology and population dynamics remain poorly understood. We provide the first assessment of the population genetic structure of longbill spearfish (Tetrapturus pfluegeri) in the [...] Read more.

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

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

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19 pages, 1858 KB

Open AccessArticle

Effects of Dietary Supplement with 17β-Estradiol on Growth Performance, Feminization Rate, and Gonadal Maturity of the Giant Freshwater Prawn, Macrobrachium rosenbergii All-Male Postlarvae

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

Fishes 2026, 11(4), 252; https://doi.org/10.3390/fishes11040252 - 20 Apr 2026

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Abstract

Monosex all-male culture of the giant freshwater prawn (Macrobrachium rosenbergii) maximizes aquaculture yield due to a male growth advantage, but direct hormonal treatment of grow-out populations poses significant food safety risks. This study evaluated the efficacy of dietary 17β-estradiol (E2) in [...] Read more.

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

(This article belongs to the Section Nutrition and Feeding)

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14 pages, 1082 KB

Open AccessArticle

Comparative Analysis of Sinking Performance and Design Parameters of Small-Scale Purse Seine Gears in Aceh and Papua, Indonesia

by Aris Widagdo, Gun-Ho Lee and Subong Park

Fishes 2026, 11(4), 251; https://doi.org/10.3390/fishes11040251 - 20 Apr 2026

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Abstract

This study presents a comparative evaluation of the sinking performance of traditional small-scale purse-seine gears used in Aceh and Papua, Indonesia, using a three-dimensional mass–spring framework validated by sea-trial data from the Java Sea. Simulations compared sinking behavior under changes in the netting [...] Read more.

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

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17 pages, 13454 KB

Open AccessArticle

Preliminary Study on Broodstock Management, Inducing Natural Spawning and Larval Rearing of Silver Pomfret, Pampus argenteus

by In Joon Hwang and Jong Cheol Han

Fishes 2026, 11(4), 250; https://doi.org/10.3390/fishes11040250 - 19 Apr 2026

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Abstract

Silver pomfret (Pampus argenteus, family Stromateidae) is a highly valuable marine fish species with significant commercial demand; however, its aquaculture remains undeveloped due to limited knowledge of captive breeding and seed production. To our knowledge, this is the first successful report [...] Read more.

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

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26 pages, 4487 KB

Open AccessArticle

Spatio-Temporal Patterns of Fish Community in the Middle and Upper Reaches of the Fuhe River After the Yangtze River Fishing Ban

by Zukun Wu, Kun Ding, Yuxuan Bao, Peng Zhang, Xinyue Ma, Maolin Hu and Shengfu Zhou

Fishes 2026, 11(4), 249; https://doi.org/10.3390/fishes11040249 - 19 Apr 2026

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Abstract

To understand the distribution characteristics of the fish community and evaluate the effectiveness of the Yangtze River fishing ban, this study selected the Fuhe River (an important tributary of the Yangtze River) as the research area. A total of 30,892 fish (belonging to [...] Read more.

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

(This article belongs to the Section Biology and Ecology)

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14 pages, 995 KB

Open AccessArticle

Earthen Pond Grow-Out of Chinese Mitten Crab Eriocheir sinensis: All-Female Culture Is Superior to Mixed-Sex and All-Male Alternatives

by Guangbao Zhang, Abdulai Merry Kamara, Zhijie Zhou, Wenbin Chen, Yang Jie, Chaoshu Zeng, Wenquan Zhou and Xugan Wu

Fishes 2026, 11(4), 248; https://doi.org/10.3390/fishes11040248 - 18 Apr 2026

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Abstract

Monosex culture has been shown to enhance farming productivity in several decapod crustaceans, and it has also been suggested that this approach holds high potential for the sustainable aquaculture of the Chinese mitten crab, Eriocheir sinensis. Pronounced sexual dimorphism in E. sinensis [...] Read more.

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

(This article belongs to the Section Sustainable Aquaculture)

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18 pages, 4967 KB

Open AccessArticle

From Core to Edge: Habitat Signatures in the Otoliths of Genidens genidens in the Southwestern Atlantic Estuaries

by Marina Paixão Gil, Mario Vinicius Condini, Maurício Hostim-Silva and Felippe Alexandre Daros

Fishes 2026, 11(4), 247; https://doi.org/10.3390/fishes11040247 - 18 Apr 2026

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Abstract

Understanding habitat use and connectivity in estuarine fishes is essential for effective conservation and management. In this study, otolith microchemistry was applied to investigate habitat use and connectivity of the estuarine catfish Genidens genidens across three estuaries in southeastern Brazil. A total of [...] Read more.

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

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

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16 pages, 3826 KB

Open AccessArticle

Effects of Dietary Supplementation with Selenium-Enriched Lactobacillus plantarum on Growth, Hepatic Antioxidant Capacity, and Intestinal Microbiota of Largemouth Bass (Micropterus salmoides)

by Chengxu Ruan, Junhao Tang, Xiufang Liu, Junwei Chen, Linxi Cheng and Xucong Lv

Fishes 2026, 11(4), 246; https://doi.org/10.3390/fishes11040246 - 18 Apr 2026

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Abstract

This study compared the effects of dietary Lactobacillus plantarum (Lpl) and selenium-enriched L. plantarum (Lpl_se) on the growth, hepatic antioxidant capacity, and intestinal microbiota of juvenile largemouth bass (initial weight 12.50 ± 0.81 g). Following a 58-day trial in an indoor rearing system, [...] Read more.

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

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

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17 pages, 10144 KB

Open AccessArticle

Ontogenetic Trophic Niche Shifts in Ctenochaetus striatus (Quoy & Gaimard, 1825) in Response to Habitat Variation: A Case Study of the Xisha Islands

by Hongyu Xie, Yong Liu, Jinhui Sun, Jianzhong Shen and Teng Wang

Fishes 2026, 11(4), 245; https://doi.org/10.3390/fishes11040245 - 17 Apr 2026

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Abstract

Against the backdrop of global coral reef degradation, benthic resource structure is shifting from coral dominance to turf algae and detritus-dominated epilithic algal matrix (EAM). As a typical detritivorous reef fish, Ctenochaetus striatus (Quoy & Gaimard, 1825) plays an important ecological role in [...] Read more.

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

(This article belongs to the Special Issue Feeding the Future: Diet Data and Ecosystem Perspectives on Fish Food Webs)

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17 pages, 2386 KB

Open AccessArticle

First Hybrid Genome Assembly of the Teleost Fish Red Cusk-Eel (Genypterus chilensis) from Oxford Nanopore and Illumina Reads: Comparative Genomic Analysis of Genypterus Species and Long Non-Coding RNA Tissue-Specific Expression

by Phillip Dettleff, Marcia Arriagada-Solimano, Vania Fuentealba, Karina Tobar, Millaray Sáez, Claudio Olave, Juan Manuel Estrada and Juan Antonio Valdés

Fishes 2026, 11(4), 244; https://doi.org/10.3390/fishes11040244 - 17 Apr 2026

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Abstract

The red cusk-eel (Genypterus chilensis) is an endemic Chilean teleost fish of significant importance to fisheries and aquaculture; however, no reference genome is available for this species. In this study, we present the first hybrid genome assembly of G. chilensis using [...] Read more.

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

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

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19 pages, 2045 KB

Open AccessArticle

Effects of Offshore Wind Farm-Associated Electromagnetic Fields on the Physiology and Behavior of Sebastes schlegelii

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

Fishes 2026, 11(4), 243; https://doi.org/10.3390/fishes11040243 - 17 Apr 2026

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Abstract

To evaluate the potential biological effects of electromagnetic fields from offshore wind farms on Sebastes schlegelii, a laboratory-controlled chronic exposure experiment was conducted using a magnet-based static magnetic field system. Each group contained 60 fish distributed across four replicate tanks, with 15 [...] Read more.

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

(This article belongs to the Special Issue Computer Vision Applications for Fisheries and Aquaculture)

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15 pages, 2831 KB

Open AccessArticle

Effects of Dietary Protein Sources on Vitellogenin of Female Largemouth Bass (Micropterus salmoides)

by Yue Tan, Yang Xu, Li Jia, Youqin Kong, Zhili Ding, Changle Qi and Qiyou Xu

Fishes 2026, 11(4), 242; https://doi.org/10.3390/fishes11040242 - 17 Apr 2026

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Abstract

To investigate the effects of three alternative protein sources—Hermetia illucens larvae meal (HIM), Chlorella meal (CM) and stickwater meal (SWM)—on the vitellogenin in female largemouth bass (Micropterus salmoides), these protein sources were used to replace 0% (control group, FM; containing [...] Read more.

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

(This article belongs to the Special Issue Effect of Dietary Supplementation on the Growth and Immunity of Fish and Shellfish—3rd Edition)

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19 pages, 2387 KB

Open AccessArticle

Exercise-Induced Epigenetic Regulation of Chchd10 Promoter Methylation Improves Muscle Morphology in Zebrafish

by Jiaxin Liu, Hui Tang, Yirong Li, Haiyang Yu, Jianguang Cai and Chongqing Wang

Fishes 2026, 11(4), 241; https://doi.org/10.3390/fishes11040241 - 17 Apr 2026

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Abstract

Skeletal muscle activity, such as exercise, enhances mitochondrial function, a process critical for ATP production through oxidative phosphorylation. Mitochondrial dysfunction, often linked to mutations in the chchd10 gene, contributes to the pathogenesis of neurodegenerative and neuromuscular diseases. Although exercise is known to improve [...] Read more.

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

(This article belongs to the Section Genetics and Biotechnology)

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4 pages, 173 KB

Open AccessEditorial

Fishmeal and Fish Oil Replacement in Aquaculture: Insights and Advances in Current Research

by Qiang Ma and Houguo Xu

Fishes 2026, 11(4), 240; https://doi.org/10.3390/fishes11040240 - 17 Apr 2026

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Abstract

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

(This article belongs to the Special Issue Development of Low-Crop, Low-Fishmeal or Low-Fish Oil Feeds for Aquaculture)

17 pages, 1236 KB

Open AccessArticle

Synergistic Effects of Achyranthes aspera and Ricinus communis Seed Extracts with an Inactivated Vaccine Enhance Growth, Immunity, and Disease Resistance in Labeo rohita

by Aiman Nadeem, Farkhanda Asad, Asma Ashraf and Tayyaba Ali

Fishes 2026, 11(4), 239; https://doi.org/10.3390/fishes11040239 - 17 Apr 2026

Viewed by 342

Abstract

Feed nutrition and rise in antibiotic resistance are growing global challenges in aquaculture, with Aeromonas hydrophila causing significant losses in the carp family. This 60-day study evaluated the potential of combining herbal seed extract (Achyranthes aspera and Ricinus communis) with inactivated [...] Read more.

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

(This article belongs to the Topic Immunology and Disease Prevention and Control in Aquatic Animals)

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14 pages, 2266 KB

Open AccessArticle

Phenotypic Variability and Adaptive Differentiation of Tench (Tinca tinca L.) from Aquaculture and Natural Populations in Southern Kazakhstan

by Rinat Barakov, Nina Badryzlova, Saule Assylbekova, Naila Bulavina, Farizat Altayeva, Almat Suyubaev and Moldir Aubakirova

Fishes 2026, 11(4), 238; https://doi.org/10.3390/fishes11040238 - 16 Apr 2026

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Abstract

This study provides a comparative analysis of phenotypic variability in the morphological traits of tench (Tinca tinca L.) reared under aquaculture conditions and those from a natural population in southern Kazakhstan. The aim of the study was to evaluate phenotypic plasticity and [...] Read more.

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

(This article belongs to the Section Biology and Ecology)

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21 pages, 14180 KB

Open AccessArticle

Embryo and Larval Developmental Staging Guides for Striped Bass

by Erimi Kendrick, Nadya Mamoozadeh, William G. Cope, Russell Borski, Robert W. Clark, Michael S. Hopper and Benjamin J. Reading

Fishes 2026, 11(4), 237; https://doi.org/10.3390/fishes11040237 - 16 Apr 2026

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Abstract

Reliable developmental benchmarks are essential for synchronizing incubation and first-feeding decisions in striped bass (Morone saxatilis) hatcheries, yet existing references are incomplete, outdated, or difficult to apply across variable temperature regimes. We developed contemporary embryo and larval developmental staging guides for [...] Read more.

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

(This article belongs to the Special Issue Advances in Fish Reproductive Physiology)

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16 pages, 6822 KB

Open AccessArticle

Fish Resource Assessment in the Huoyanshan Waters of Poyang Lake Using DIDSON and Deep Learning Models

by Wei Shen, Zhaowei Yin, Bao Zhang, Lekang Li, Enze Qian and Xiaoling Gong

Fishes 2026, 11(4), 236; https://doi.org/10.3390/fishes11040236 - 16 Apr 2026

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Abstract

To scientifically assess the fish resource status and spatial distribution in the Huoyanshan waters of Poyang Lake for the conservation of endangered species like Coilia nasus, an acoustic survey was conducted using a dual-frequency identification sonar (DIDSON) in July 2024. Fish targets [...] Read more.

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

(This article belongs to the Special Issue Technology for Fish and Fishery Monitoring—2nd Edition)

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20 pages, 7157 KB

Open AccessArticle

Expression Patterns of Genes Involved in Sexual Development of Turbot (Scophthalmus maximus): A Histological Analysis by In Situ Hybridization on Differentiated Ovarian and Testicular Tissue

by Fátima Adrio, Xoana Taboada, Paulino Martínez and Ana Viñas

Fishes 2026, 11(4), 235; https://doi.org/10.3390/fishes11040235 - 16 Apr 2026

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Abstract

Genes involved in sexual development have been identified in many teleost fishes, including the turbot, a flatfish of high commercial value in aquaculture. In this species, a major sex determination (SD) Quantitative Trait Locus has been identified, and Sox2 has been proposed as [...] Read more.

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

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21 pages, 9544 KB

Open AccessArticle

Effects of Different LED Lights on the Growth Performance and Serum Lysozyme Activity of Common Carp Cyprinus carpio and Bacterial Communities in a Closed Recirculating System

by Phan Trong Binh, Satoshi Hori, Nguyen Thi Dang, Katsuhisa Uchida and Yousuke Taoka

Fishes 2026, 11(4), 234; https://doi.org/10.3390/fishes11040234 - 15 Apr 2026

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Abstract

We evaluated the effect of our light-emitting diode (LED) light treatments (blue, peak at 468 nm; green, peak at 537 nm; red, peak at 630 nm; and white light) on the growth performance and serum lysozyme activity of the common carp Cyprinus carpio [...] Read more.

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

(This article belongs to the Special Issue Fish Health and Welfare in Aquaculture and Research Settings)

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15 pages, 4921 KB

Open AccessArticle

Evaluation of Hypoxia Tolerance and Cloning-Expression Analysis of Related Genes in Hybrid Fish Derived from Megalobrama amblycephala × Xenocypris davidi Bleeker

by Zhong Tang, Xinxin Yu, Xin Chen, Junwen Liang, Yangyang Tu, Zhifeng Zhou, Faxian Yu, Chun Zhang, Siyu Fan and Min Tao

Fishes 2026, 11(4), 233; https://doi.org/10.3390/fishes11040233 - 15 Apr 2026

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Abstract

The diploid distant hybrid (2nBY) derived from female blunt snout bream (Megalobrama amblycephal, BSB) × male Bleeker’s yellow tail (Xenocypris davidi Bleeker, YT). To investigate the hypoxia tolerance and the regulatory mechanisms of hypoxia-inducible factor-1α/2α (hif-1α/2α) [...] Read more.

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

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

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22 pages, 7037 KB

Open AccessArticle

Projected Impacts of Extreme Drought on Tilapia Aquaculture in Guangdong, China, Under SSP Scenarios: Climate-Yields Modeling Approach Using Loss Function

by Shunxiang Yang, Yingli Zhang, Zefang Liao and Dengke Cao

Fishes 2026, 11(4), 232; https://doi.org/10.3390/fishes11040232 - 15 Apr 2026

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Abstract

Global warming presents urgent challenges for tilapia aquaculture. This study introduces a tailored loss function to assess long-term impacts under extreme drought, using historical drought data in China as a baseline. The TaiESM1 climate model within the CMIP6 framework is applied to project [...] Read more.

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

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

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2 pages, 131 KB

Open AccessCorrection

Correction: Liang et al. Integration of Biofloc and Ozone Nanobubbles for Enhanced Pathogen Control in Prenursery of Pacific White Shrimp (Penaeus vannamei). Fishes 2025, 10, 218

by Qinlang Liang, Yazhi Luan, Zhengwen Wang, Jiangbo Niu, Yasong Li, Hua Tang, Zengting Li, Songming Zhu and Gang Liu

Fishes 2026, 11(4), 231; https://doi.org/10.3390/fishes11040231 - 15 Apr 2026

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Abstract

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

(This article belongs to the Section Welfare, Health and Disease)

15 pages, 16360 KB

Open AccessArticle

Socio-Economic Characterization and Operational Patterns of Multi-Gear Artisanal Fisheries in Pangandaran Coastal Waters, West Java, Indonesia

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

Fishes 2026, 11(4), 230; https://doi.org/10.3390/fishes11040230 - 15 Apr 2026

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Abstract

Small-scale fisheries constitute the backbone of coastal livelihoods in Indonesia, yet comprehensive socio-economic data remain limited for effective management. This study characterizes the operational and socioeconomic patterns of multi-gear artisanal fisheries in the Pangandaran coastal waters of West Java, Indonesia. A cross-sectional survey [...] Read more.

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

(This article belongs to the Special Issue Sustainable Fisheries Dynamics)

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13 pages, 2853 KB

Open AccessArticle

The Potential Drug Target (Glycolysis Pathway) of the Spore Stage of the Pathogen Enterocytozoon hepatopenaei in Shrimp Farming

by Bo Zhu, Juan Feng, Dong Qian, Ping Zhuang, Changkao Mu, Jiong Chen and Rongrong Ma

Fishes 2026, 11(4), 229; https://doi.org/10.3390/fishes11040229 - 15 Apr 2026

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Abstract

Enterocytozoon hepatopenaei (EHP) is a specialized parasitic microsporidian that causes significant economic losses to the shrimp farming industry. The glycolysis pathway plays an important role in the survival of EHP spores in vitro. In this study, key enzyme genes involved in the glycolysis [...] Read more.

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

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

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16 pages, 2768 KB

Open AccessArticle

Metabolomic Profiling of Intestinal Contents in Rice Paddy-Cultured Eriocheir sinensis: Linking Gut Microbiota Composition with Metabolic Pathway Dynamics

by Jinpeng Zhang, Yayu Wang, Yunxiao Yang, Hong Lin, Yuhong Yang and Dayan Hu

Fishes 2026, 11(4), 228; https://doi.org/10.3390/fishes11040228 - 14 Apr 2026

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Abstract

Rice–crab coculture, as China’s third-largest integrated farming model, is pivotal for sustainable Chinese mitten crab aquaculture. This study conducted untargeted metabolomics and 16S rRNA gene sequencing on gut contents of crabs from rice fields and ponds, integrating metabolic and microbial profiles. We aimed [...] Read more.

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

(This article belongs to the Section Aquatic Invertebrates)

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17 pages, 1090 KB

Open AccessArticle

Feeding Physiology of Crassostrea gasar (Dillwyn, 1817) on Isochrysis galbana and Biofloc Diets

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

Fishes 2026, 11(4), 227; https://doi.org/10.3390/fishes11040227 - 14 Apr 2026

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Abstract

Understanding the feeding physiological mechanisms of determined oyster species is fundamental for adaptation and growth stabilization, aiming for gains in aquaculture production. To assess its potential for Integrated Multi-Trophic Aquaculture (IMTA) with shrimp, we analyzed the feeding physiology of the mangrove oyster Crassostrea [...] Read more.

Understanding the feeding physiological mechanisms of determined oyster species is fundamental for adaptation and growth stabilization, aiming for gains in aquaculture production. To assess its potential for Integrated Multi-Trophic Aquaculture (IMTA) with shrimp, we analyzed the feeding physiology of the mangrove oyster Crassostrea gasar. In this study, we determined the feeding physiology of the mangrove oyster Crassostrea gasar, a commercially important species in tropical Brazil, under two diets, live microalgae (ISO—Isochrysis galbana) and biofloc (BFT), which were tested at four concentrations (10, 20, 30, and 40 mg L⁻¹), to establish whether this species can effectively utilize BFT as a food source. Results indicated that ISO diet promoted superior filtration, characterized by a higher proportion of feces (F), suggesting a reduced need for intensive particle selection. Both clearance (CR) and filtration (FR) rates peaked at 30 mg L⁻¹ before declining, suggesting a physiological threshold for this diet. In contrast, the BFT diet elicited higher CR and FR values but triggered excessive pseudofeces (PF) production and low net organic selection efficiency (NOSE). This suggests high particle rejection and limited nutritional assimilation. In conclusion, while C. gasar can process BFT, it is metabolically disadvantageous as a sole food source. For an optimal performance, I. galbana concentrations should be maintained at or below 30 mg L⁻¹. 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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13 pages, 2433 KB

Open AccessArticle

Development of a Two-Set Multiplex PCR System for Rapid Discrimination of Seven Commercially Important Cuttlefish Species Using COI-Derived SNP Markers

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

Fishes 2026, 11(4), 226; https://doi.org/10.3390/fishes11040226 - 12 Apr 2026

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Abstract

Reliable identification of seafood species is critical for fisheries management and product authentication, especially when morphological characteristics are lost during processing. In this study, a multiplex PCR system was developed to distinguish seven cuttlefish species (six Sepia spp. and Sepiella inermis) commercially [...] Read more.

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

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

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22 pages, 1769 KB

Open AccessArticle

Seasonal Variation in the Body and Biochemical Condition of Gonads in Female Common Sardine (Strangomera bentincki)

by Fabián Guzmán-Rivas, Juan Carlos Ortega, Sergio Mora and Ángel Urzúa

Fishes 2026, 11(4), 225; https://doi.org/10.3390/fishes11040225 - 12 Apr 2026

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Abstract

Understanding the reproductive physiology of marine fish is critical for sustainable fisheries management, particularly under environmental variability. This study evaluated seasonal changes in body parameters (condition factor, Kn, and gonadosomatic index, GSI, as proxies for body condition and reproductive status, respectively) and biochemical [...] Read more.

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

(This article belongs to the Section Physiology and Biochemistry)

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17 pages, 6423 KB

Open AccessArticle

Gut Microbiota Composition and Predicted Functional Profiles of Fishes Along an Urbanization Gradient in Shanghai’s Suzhou River, China

by Shuo Feng, Hua Xue, Xirong Lin, Ana Wu and Wenqiao Tang

Fishes 2026, 11(4), 224; https://doi.org/10.3390/fishes11040224 - 10 Apr 2026

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Abstract

Ongoing urbanization continuously reshapes water quality, habitat structure, and biological communities in river ecosystems; however, its impacts on host-associated microbial communities remain poorly documented. The fish gut microbiota, a critical interface between the aquatic environment and host physiology, is widely recognized as an [...] Read more.

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

(This article belongs to the Section Biology and Ecology)

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