Fishes

Antibiotics are widely recognized as significant chemical pollutants that enter the environment and ultimately the food chain. They are extensively used in both aquaculture and terrestrial animal breeding. Antibiotic residues in cultured fish pose significant public health risks, including the potential for antimicrobial resistance and adverse health outcomes. This review examines the widespread use of antibiotics in aquaculture, highlighting key challenges such as the lack of reliable data on antibiotic consumption in many regions as well as variability in regulatory enforcement. While strict regulations in European countries help to mitigate risks, the growing, often unregulated use of antibiotics in low- and middle-income countries exacerbates concerns over food safety. This paper provides an in-depth analysis of global regulatory frameworks and the impact of antibiotic residues on public health, and it offers recommendations for improving the monitoring, regulation, and responsible use of antibiotics in aquaculture in order to ensure safer food products from farmed fish. It contributes to a deeper understanding of the global scope of antibiotic misuse in aquaculture and points to an urgent need for more effective management practices. Full article

Euspira gilva, a member of the family Naticidae, is predominantly found in intertidal soft mud, sandy soil, and sandy seabeds along the coast of China, where it is valued for its nutritional richness and significant economic value. This study presents a comprehensive transcriptome sequencing and analysis of E. gilva specimens from the Lianyungang area, yielding 3385 high-quality isoform sequences and 3310 non-redundant transcripts. Annotation against various databases, including NR, Swiss-Prot, KEGG, KOG, eggNOG, GO, and Pfam, successfully annotated a significant number of transcripts. A total of 7929 simple sequence repeat (SSR) loci were identified, with single nucleotide repeats predominating at 85.0%. Predictive analysis of coding DNA sequences (CDS) resulted in 1340 BLAST comparisons, while ESTScan predicted 840. Further, 530 long non-coding RNAs (lncRNAs) were identified through the application of the CPC2, CNCI, Pfam, and PLEK algorithms. The highest overall sequence similarity in the NR database was observed with Pomacea canaliculata, a freshwater species, but with a similarity of only 36.6%, indicating a unique genetic makeup of E. gilva. The KEGG database annotation revealed a predominance of signal transduction pathways, particularly the PI3K-Akt signaling pathway, with 29 non-redundant transcripts encoding key genes such as IGH (immunoglobulin heavy chain), PCK (phosphoenolpyruvate carboxykinase), COL2A (collagen, type II, alpha), ITGB1 (integrin beta 1), and GNG7 (guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-7). These genes play crucial roles in cellular processes, including cell growth, transcription, translation, proliferation, movement, and glycogen metabolism. The findings of this research elucidate the full-length transcriptome profile of E. gilva, thereby establishing a foundational dataset and providing valuable insights for the species’ aquaculture, health management, conservation efforts, and future molecular biological investigations. Full article

For many aquatic species, vision is important for detecting prey, predators, and conspecifics; however, the potential impacts of visual cues from offshore wind turbines have not been investigated in these crucial contexts. There is the possibility of visual cues, originating from moving wind turbine blades, propagating through the air–water interface to impact visually sensitive species. Two classes of visual cues are possible: direct motion cues originating as light reflected from moving turbine blades and indirect cues resulting from an interruption of direct sunlight causing dynamic shadowing when the sun, blade, and receptor are aligned. In both cases, the propagation of cues across the air–water interface is governed by physical principles but modulated in potentially complex ways by the aspects of the local environment that vary with time. Evidence for the extent of the exposure of aquatic organisms to the visual cues arising from moving turbine blades and for the potential response of receptor organisms is sparse. This study considers the physics involved to support the formulation and testing of robust biological hypotheses. Marine migratory salmonid species are considered as an example species because their behaviour in the marine environment is relatively well documented. This study concludes that the aquatic receptor organisms present in the uppermost layer of the sea in the vicinity of wind turbines are potentially exposed to direct motion cues originating from moving turbine blades and also, when the sun elevation angle is greater than ca. 20°, to dynamic shadowing cues. Full article

The radiation of cichlid species in the East African Great Lakes is remarkable and rapid. The population genetics of two deep-water Cyphotilapia species along the east coast of Lake Tanganyika from Burundi to southern Tanzania was determined using ddRAD-seq. A combination of ADMIXTURE, PCA, genome polarization, and 2D site frequency spectrum analyses confirmed the presence of two species, C. frontosa in the north and C. gibberosa in the south, as documented in other studies. We also found evidence of a potential hybrid zone connecting the two species at a sharp genetic cline centered in the middle of the lake and apparent introgression in both directions, but predominantly from ‘gibberosa’ into ‘frontosa’. The highest proportion of introgressed ‘gibberosa’ ancestry was present in the southernmost populations of C. frontosa collected near Karilani Island and Cape Kabogo. At the intra-specific level, there was support for between 1 and 3 populations of C. frontosa, whereas the results indicated only a single homogeneous population of C. gibberosa. The presence of different morphs in the lake despite the low levels of heterozygosity suggests that a small number of loci may be involved in the morphological variation and/or that there is a more complex interplay between genetics and the environment in different locations. Full article

The present work aimed to evaluate and mathematically model the effect of temperature on Morganella morganii growth and histamine formation in farmed mullet (Mugil cephalus) during refrigerated storage (at constant temperatures, T = 0, 2.5, 5, 10, and 15 °C) and to validate the developed models at non-constant temperature conditions (effective temperature T_eff = 7.4 °C). Shelf life evaluation of chilled mullet was also carried out based on microbial spoilage, sensory degradation, and total volatile nitrogen (TVB-N) determination. Spoilage of mullet during refrigerated storage was co-dominated by Pseudomonas spp. and Enterobacteriaceae growth. Sensory rejection (score 5 for overall impression) and the end of shelf life coincided with a total microbial load of 8 log cfu/g. The shelf life of chilled mullet was estimated at 15, 11, 7, 3, and 1.5 days at 0, 2.5, 5, 10, and 15 °C, respectively. At T 0–5 °C, the time of sensory rejection coincided with TVB-N concentrations of 10.2–12.3 mg·100 g⁻¹, and at 10–15 °C, the samples were sensorially rejected before TVB-N development. At storage temperatures < 5 °C, sensory rejection was observed well before histamine levels reached a concentration of 50 mg/kg fish flesh. However, when abusive temperatures prevail, histamine should be considered as a risk factor for the human consumption of mullet. Full article

The European eel (Anguilla anguilla) undergoes significant morphological and physiological changes during its transition from the yellow to the silver stage, which are critical for its long-distance spawning migration. This study aimed to investigate these changes in European eels from the Asi River, located in Hatay, Türkiye, during their silvering process. A total of 96 eels were sampled in February 2019, and various morphometric measurements, including total length, body weight, eye dimensions and height, and pectoral fin lengths, were taken. Liver and gonad weights were also measured to assess the hepatosomatic index (HSI). The length–weight relationship for silver eels was described by the equation, W = 0.0072 × L^2.732, with silver-stage eels showing a higher growth rate compared to yellow-stage eels, which had a relationship of W = 0.0184 × L^2.397. The average total length of silver eels (431.2 ± 16.7 mm) was significantly greater than that of yellow eels (382.4 ± 11.9 mm). Additionally, pectoral fin length was significantly longer in silver eels (20.8 ± 1.1 mm) compared to yellow eels (14.8 ± 0.9 mm). The hepatosomatic index (HSI) for silver eels was also found to be higher than for yellow eels, indicating increased liver size as an adaptation for energy storage during migration. Eye height, a key indicator of silvering, showed a substantial increase during the transition, with silver-stage eels having an average eye height of 5.3 ± 0.2 mm compared to 4.2 ± 0.1 mm in yellow-stage eels. Full article

The aim of this study was to evaluate the effect of predominantly chemoautotrophic and heterotrophic biofloc systems on ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), and planktonic microorganisms in an integrated Penaeus vannamei and Oreochromis niloticus integrated multitrophic culture. Shrimp and tilapia were stocked at a density of 400 shrimp m⁻² and 45 fish m⁻³, respectively. The trial consisted of two biofloc treatments, with three replicates each: chemoautotrophic and heterotrophic. The identification and quantification of the planktonic microorganisms (ciliates, flagellates, microalgae, and total bacteria) and nitrifying bacteria were carried out through direct counting and fluorescence in situ hybridization, respectively. At the end of the trial, heterotrophic treatment had resulted in higher total abundance of bacteria. The relative abundance of AOB and NOB in relation to the total abundance was less than 0.1% for both treatments. The system was dominated by flagellates in both treatment groups. The abundance of microalgae and ciliates was higher with chemoautotrophic treatment. After 43 days, the shrimp weights were higher in the chemoautotrophic group, while the final weights of the tilapia were not significantly different between the two treatments. The type of biofloc system (Chemoautotrophic vs. Heterotrophic) did not significantly alter the establishment of AOB and NOB in a Penaeus vannamei and Oreochromis niloticus integrated multitrophic culture. The two treatments proved to be equally efficient for maintaining good water quality, but the chemoautotrophic treatment resulted in better shrimp growth. Thus, our study demonstrated that chemoautotrophic biofloc is a promising approach in integrated multitrophic aquaculture. Full article

The spread of non-native species threatens biodiversity and exacerbates societal challenges like food security. To address this, effective conservation programs require detection methods that are easy to implement, accurate, and non-invasive. Over the past 15 years, environmental DNA (eDNA) techniques have gained popularity, surpassing traditional sampling methods. In this context, our study focused on tracking the invasive host–pathogen complex Pseudorasbora parva and Sphaerothecum destruens using eDNA metabarcoding. We collected water samples from freshwater canals over five months in the Camargue region, and once in Corsica Island, both in southern France. Total DNA was extracted from filtered water samples, and PCR-amplicons were sequenced using Illumina or Nanopore technologies. Our results revealed a high detection rate of P. parva in lentic ecosystems, aligning with habitat preferences of this small freshwater fish. Additionally, the detection rate in Camargue increased in May and June, likely due to the peak of the spawning season, which leads to more DNA being released into the environment (i.e., concentration and interaction of individuals). While eDNA successfully detected this invasive fish, we were unable to detect its cryptic fungal parasite, S. destruens, highlighting the challenges of identifying intracellular and cryptic fungal pathogens through eDNA methods. Full article

The potential probiotic properties of three Bacillus strains were studied. A probiotic supplement for the African catfish Clarias gariepinus was produced via the solid-state fermentation protocol and incorporated into the fish feed for a period of seven weeks. Since the 36th day of the experiment, all experimental groups had a statistically significant increase in their weight gain than the control group. The maximum weight gain observed in fish fed the probiotic-supplemented feed was 29.16% higher than that of the control group, and the maximum feed conversion rate improvement was 24%. Cell-free extracts from these strains showed antioxidant (11.55–27.40%) and DNA-protective (45.33–61.83%) activity in a series of in vitro biosensor tests. Further investigation into the antimutagenic activity of the strains revealed that two of them reduced the level of induced mutagenesis in an Escherichia coli model (by 33.58% and 54.35%, respectively). We also assessed the impact of probiotic strains on the expression of several key genes in the host (C. gariepinus), including hsp70, cxc, tnfα, il1β, and lysC. More than a 10-fold increase in expression rates was observed for hsp70 in gonads and liver; for cxc in muscles and gonads; for tnfα in brain, gills, and liver; for il1β in the brain, gills, gonads, and liver; and for lysC in gills, gonads, liver, and muscles. This study provides evidence that probiotics exhibiting antioxidant and antimutagenic properties can provide significant benefits in vivo within aquaculture systems. The molecular effects of these probiotics appear to be complex and tissue-specific, with both upregulation and downregulation of immune system genes observed. Nevertheless, at the organismal level, the impact was unequivocally positive in terms of aquaculture objectives, manifested as enhanced body weight gain in the fish. Consequently, these Bacillus strains warrant serious consideration as potential probiotics for this species. Full article

Our study investigates the trophic ecology of the anchoveta (Engraulis ringens). The anchoveta plays a key role in the Greater Humboldt Ecosystem and is extensively exploited by countries from the south-eastern Pacific Ocean. For a comprehensive study of trophic ecology, we employed a combined approach that included stomach content analysis, stable isotope analysis, and scaled mass index of body condition. Our results showed that the multivariate composition of the diet varies significantly between life stage and fishing zones in Chile. Copepods and euphausiids emerged as the dominant prey found in the stomachs across all fisheries zones. Stable isotope analysis revealed significant differences among different zones. The scaled mass index values were higher in the northern zone compared to the southern zones, for both juveniles and adults. This research carries significant implications for fisheries management and conservation efforts, such as the development of targeted management strategies that address variations in the trophic structure of anchoveta across different life stages and fishing zones. Full article

Live transportation is a critical component of fish farming and hatchery release. To optimize hatchery-release techniques and improve the survival rate of marbled rockfish (Sebastiscus marmoratus, Cuvier 1829) juveniles, the effects of varying transport durations (2, 4, 6, and 8 h) and densities (60, 90, 120, and 150 kg m⁻³) on the physiological indicators of the fish and water quality were investigated under controlled laboratory conditions. We found that as transport duration and density increased, water quality significantly deteriorated, with ammonia nitrogen levels rising and dissolved oxygen content and pH levels decreasing. Physiological indicators including levels of lactate, cortisol, and malondialdehyde and activities of superoxide dismutase, alkaline phosphatase, and glutamate oxaloacetate transaminase notably increased, indicating that the fish experienced heightened stress during transport. Additionally, the mortality rate of juveniles increased significantly with increasing density and transport duration. The high mortality rate might be associated with sustained elevated cortisol levels and liver damage. Our results are helpful for determining the optimal transport conditions for S. marmoratus juveniles and also provide valuable insights for improving transport techniques for other aquatic animal species. Full article

In this study, to investigate the quality of wild and farmed frozen southern bluefin tuna, physicochemical analyses and sensory evaluations were conducted. Principal component analysis was then performed using the results obtained to examine the correlation between the bluefin tuna’s taste characteristics and physicochemical properties. The sensory evaluation suggested differences in texture and acidity between wild and farmed fish, whereas the principal component analysis indicated differences in fatty acid and amino acid composition. Wild fish contained higher levels of docosahexaenoic acid and monounsaturated fatty acids, while farmed fish had higher levels of saturated fatty acids. Regarding free amino acids and dipeptides, wild fish had higher levels of anserine and alanine, whereas farmed fish showed higher levels of glutamine and histidine, and acidity was observed in farmed fish. Furthermore, based on the results of the principal component analysis, it was inferred that the content of inosinic acid, which is considered an umami component in fish, may have a low impact on palatability. These factors were suggested to influence the differences between wild and farmed tuna. Full article

According to EuroStat data, the recorded landings of fisheries products from European waters were estimated at about 6 million tons in 2001, down to 3.2 million tons in 2022. This gradual decline slowed after the entering into force of the reform of the European Common Fisheries Policy (CFP) at the end of 2013, but was followed by a steeper decline after 2018. This is reflected in the last assessment of the Scientific Technical and Economic Committee for Fisheries (STEPF), noting that despite progress in the NE Atlantic management, 41% of the assessed stocks in 2022 were outside safe biological limits, down from 80% in 2003. Improvements in the Mediterranean are significantly slower. A warming ocean provokes the measurable poleward migration of species and adds stress to predator–prey relations in all European seas. Within this general picture, the broad-brush landscape is influenced by policy applications more in favour of industrial exploitation and regulatory and market environments, making it very hard for many small-scale fishers (SSFs) to remain in business, let alone attract younger successors for generational transition. In crowded marine spaces, it is a challenge to allocate access rights fairly between fisheries, exclusion zones for resource and habitat protection and much-needed ecosystem recovery, platforms for fossil exploitation, wind farms, underwater cables and recreational uses. Two examples of local initiatives with faunal recovery potential in the Mediterranean are briefly presented as a bottom-up complement to more top-down management approaches. They are spearheaded by artisanal fishers, who seek to restore spawning grounds and other coastal habitats as a way to procure enough fish and other complementary activities to secure their livelihoods in the future. They are supported by local scientists and nature conservation organisations. While promising, this is still rather the exception. Here, it is argued that trust-building between artisanal fishers, conservationists and scientists, and greater systemic support to SSFs by governments, increase chances for the urgently needed structural shifts that deliver the reversal in the ongoing decline in biodiversity and ocean productivity that all aspire to, to ensure sustained social and economic benefits. Full article

Portuguese oyster (Magallana angulata) is one of the most important shellfish species worldwide. Although significant improvements in growth have been achieved through artificial selection breeding, the genetic basis underlying these traits remains unclear. Thus, this study aimed to (i) estimate variation and heritability for growth-related traits and (ii) identify SNPs and candidate genes associated with growth traits in Portuguese oyster. Five growth-related traits, including shell height (SH), shell length (SL), shell width (SW), whole weight (WW), and soft tissue weight (STW), were measured and analyzed in 114 one-year-old individuals from a cultivated population in Fujian Province, China. Through whole-genome sequencing and genotyping, we obtained 8,183,713 high-quality SNPs. Based on the genomic relationship matrix, heritability for the five traits was estimated, ranging from 0.071 to 0.695. Through genome-wide association analysis (GWAS), a total of nine SNPs were identified as significantly or suggestively associated with one of the growth-related traits, each explaining phenotypic variation ranging from 14.13% to 18.56%. Differentially expressed genes (DEGs) between individuals with extreme phenotypes were identified using comparative transcriptome analysis, ranging from 868 to 2274 for each trait. By combining GWAS and comparative transcriptome analysis, a total of seven candidate genes were identified, with biological functions related to growth inhibition, stress response, cell cycle regulation, and immune defense. The associations between the candidate genes and the growth-related traits were validated by using single-marker association analysis in other populations. Based on SNPs in these candidate genes, 16 haplotypes associated with growth-related traits were obtained. This study contributes to a deeper understanding of the genetic mechanisms of growth traits, and provides a theoretical basis and genetic markers for the breeding of fast-growing strains of the Portuguese oyster. Full article

Brasília, Distrito Federal, is among the Brazilian cities with the highest number of tilapia farms, with around 660 farms, of which 112 are commercial. The aim of this study was to validate a health characterization model for commercial tilapia production using the production chain in the Distrito Federal (DF), one of Brazil’s 27 federative units, by applying a semi-structured questionnaire. A total of 112 farms were categorized according to the degree of vulnerability to the introduction of pathogens and the risk of dissemination using two weighted scorecard tables that evaluated 15 items each. After calculating the mean between the two variables, the farms were classified from A (insignificant risk) to D (high risk). Most of the commercial tilapia farms in the Distrito Federal were categorized as B (39; 34.8%) and C (53; 47.3%), representing low and medium risk, respectively. When comparing the different commercial groups, a significant difference (p < 0.05) was observed in the mean scores between closed-system fattening farms and both semi-closed fattening farms and pay-to-fish farms. Closed-system fattening farms, such as those using biofloc, aquaponics, and recirculation aquaculture systems, showed the lowest vulnerability to pathogen entry and the lowest risk of disease spread. The study’s findings provide valuable health information for the official veterinary service of the DF, enabling the categorization of farms, identification of production units, and determination of the most vulnerable strata. Furthermore, the model can be easily applied by private companies and by official veterinary services in other states or countries with significant tilapia production that need to implement risk-based surveillance programs for tilapia farms. Full article

The Chinese mitten crab (Eriocheir sinensis) is an economically important crustacean. With the development of the E. sisnensis industry, precocity has become a significant challenge in juvenile crab culturing. In this study, the eyestalks of female E. sinensis from precocious (PE) and normal juvenile (NE) groups were used for proteome and metabolome analyses. In total, 731 up-regulated and 657 down-regulated differentially expressed proteins (DEPs) were identified in the PE and NE groups. In addition, 110 differentially expressed metabolites (DMs) were up-regulated and 256 were down-regulated in the PE group. An integrated analysis showed 5667 significant correlations between the metabolites and proteins and 109 common pathways in the proteome and metabolome. The proteins were mostly associated with the mechanistic target of rapamycin (mTOR) pathway, longevity regulation, autophagy, and the pyrimidine and purine metabolism pathways. The metabolites were primarily enriched in amino acid and lipid metabolisms. These results demonstrated the differences in the PE and NE groups at two omics levels and will be useful for the E. sinensis industry. Full article

Carnosine is a natural dipeptide made up of L-histidine and β-alanine which is rich in muscle tissues and has multiple physiological functions. The current research aimed to investigate the effects of varied carnosine concentrations in low-fishmeal feed on the growth, muscle antioxidant capacity and flesh quality of orange-spotted grouper. Carnosine was supplemented at doses of 0, 10, 20, 40, 80, 160, and 320 mg/kg in low-fishmeal feed. Seven groups with three tanks of fish (11.4 ± 0.1 g/fish) were allotted one of the diets during the 8-week feeding trial. The growth rate, body protein content, muscle activities of superoxide dismutase and catalase, and muscle adhesiveness showed positive linear response and/or an open upward parabola with increasing carnosine concentrations, with a peak at 160 mg/kg of carnosine. Feed utilization, serum total protein content, gut trypsin activity, muscle glutathione peroxidase, total antioxidant capacity, muscle hardness, gumminess, chewiness and resilience followed the same pattern as the growth rate, reaching a peak at 320 mg/kg of carnosine; while the opposite trend was observed, reaching a minimum at 320 mg/kg for muscle malondialdehyde and 160 mg/kg for muscle liquid and water loss. The results indicated that appropriate carnosine addition could improve growth performance, muscle antioxidant capacity and flesh quality of grouper. The suitable inclusion concentration was estimated to be 195.14 mg/kg to achieve the best percent weight gain. Full article

The impact of dietary protein and lipid levels on the growth performance, feed utilization, and serum biochemical indices of Furong crucian carp was examined. Five hundred and forty carp (2.35 ± 0.08 g) were randomly assigned to nine groups and fed diets with three different protein levels (30.0, 35.0, and 40.0%) and three different lipid levels (4.0, 7.0, and 10.0%) for 60 days. The current findings revealed that the interaction effect between dietary lipid and protein levels exhibited significance for the final average weight (FAW), weight gain rate (WGR), specific growth rate (SGR), feed efficiency (FE), energy deposition rate (EDR), whole-fish energy, ash, and fat content (p < 0.05). Specifically, there was a significant reduction in FAW, WGR, and SGR with increasing dietary fat supplementation. Conversely, FE, EDR, and protein efficiency ratios were significantly decreased with increasing dietary protein levels (p < 0.05). Furthermore, serum albumin and globulin levels exhibited significant increases in response to dietary lipid inclusion (p < 0.05). The findings collectively indicate that Furong crucian carp fed a diet comprising 4% lipid and 30% protein exhibited the optimal growth and feed utilization. Conversely, excessive protein and lipid supplementation were detrimental to growth and resulted in the aggravation of metabolic disorders. Full article