Flatfish Species Research Articles

The complete mitochondrial genome sequence of Rikuzen flounder, Dexistes rikuzenius (Jordan & Starks, 1904)

In this study, the complete mitochondrial genome of the Rikuzen flounder (Dexistes rikuzenius) using next-generation sequencing and bioinformatics analysis is presented. The mitogenome was found to be a circular molecule 17,494 bp in length, containing 13 protein-coding genes (PCG), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one control region (D-loop). Proportional nucleotide composition was A: 28.80% (5,039 bp), T: 26.51% (4,638 bp), C: 28.72% (5,025 bp) and G: 15.96% (2,792 bp), with a combined A+T content of 55.32%. The phylogenetic relationships of the taxon with 19 other flatfish species in the order Pleuronectiformes were then analyzed based on the 13 PCGs. Dexistes rikuzenius was most closely clustered with Cleisthenes herzensteini within this order, suggesting a close relationship.

A Quantitative Histologic Analysis of Oogenesis in the Flatfish Species Pleuronectes platessa as a Tool for Fisheries Management.

The following paper gives a detailed description of the oogenesis cycle for the European Plaice (Pleuronectes platessa), from oogonia to post-ovulatory follicle, including ovarian follicle and zona pellucida sizes. Noteworthy particularities were the difficulty in identifying cortical alveoli due to their very small size. Quantitative histology (stereology) on histological slides was used to determine a first size at maturity for females from the English Channel, which was found to be smaller compared to the literature (19 cm). Stereology also determined a first spawning event starting in January, with a peak in February and ongoing until March. Moreover, the use of stereology showed misclassifications for individuals categorized into a maturity phase using a macroscopic visual method. Misclassifications were found with individuals that had spawned (D) but were put under the immature (A) phase, and individuals in development (B) classified under D.

Transcriptomic and behavioral studies reveal that glutamate receptors are involved in depressive-like behavior in adult olive flounder Paralichthys olivaceus

Olive flounder (Paralichthys olivaceus), a marine demersal flatfish species, exhibits obvious timid and depressive-like characteristics. Adult olive flounder bury themselves in the sand and present motionless behavior. However, the detail mechanism of regulating the motionless behavior is not fully understood. In this study, using adult group (AG) and juvenile group (JG) flounder as a model, we compared the locomotor activity of AG and JG flounder, and analyzed the transcriptomic expression profiles in the spinal cord by RNA-seq methods. The behavioral experiment showed that AG flounder displayed lower locomotor activity. Transcriptome analysis found a total of 1711 significantly differential expressed genes (DEGs), among which 818 genes were up-regulated and 893 genes were down-regulated in AG flounder compared with JG flounder. Specifically, locomotor behavior related genes (parvalbumin, urotensin II and creatine kinase) were down-regulated. Meanwhile glial fibrillary acidic protein, the biomarkers of astroglial pathology, and glutamatergic synaptic genes were significantly up-regulated in AG flounder. In addition, Gene Ontology (GO) enrichment analysis revealed that DEGs enriched in peptide biosynthetic process, translation procession were down-regulated in the AG flounder. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that ribosome, oxidative phosphorylation and glutamatergic synapse pathway were over-represented. After treatment with antagonist of glutamate receptor LY341495, flounder more often swam out of the sand and displayed significantly more off-bottom swimming behavior, suggesting the anti-depressive effect of LY341495. Taken together, in combination with behavioral tests and transcriptomic analyses, we conclude that the glutamate receptor in spinal cord plays an important role in timid and depressive-like behavior in flounder.

Reproductive behavior of Atlantic halibut (Hippoglossus hippoglossus) interpreted from electronic tags.

Reproductive timing, location, and behavior are important characteristics that determine marine population dynamics, structure, and resilience to threats, including fishing and climate change. It is challenging to evaluate factors driving variability in these reproductive traits in wild fishes because of the difficulty observing individuals in their natural environments. In the present study, we used high-resolution depth, temperature, and acceleration time series recorded by pop-up satellite archival tags to (1) identify and characterize patterns in depth and acceleration that may be indicative of spawning events in large Atlantic halibut (Hippoglossus hippoglossus), and (2) estimate the effects of individual traits (body size and sex) and environmental factors (location and temperature) on spawning time and frequency. Unique rapid rises observed in the winter depth profiles were interpreted as spawning events. The initiation of the first presumed spawning rise was negatively correlated to water temperature experienced during the prespawning season, suggesting that currently increasing water temperature in the Gulf of St. Lawrence may induce phenological change in halibut spawning time. The number of rises of batch-spawning females was unrelated to female body size. The present study demonstrates how electronic tagging can be used for in-depth characterization of timing, location, and behaviors associated with spawning in a large flatfish species. Such information can inform spatiotemporal management and conservation measures aiming to protect species from directed fishing and by-catch during spawning.

Geometric morphometric analysis of Pleuronectiformes vertebrae: A new tool to identify archaeological fish remains?

Flatfish (Pleuronectiformes) vertebrae are difficult to identify to species due to the lack of diagnostic features. This has resulted in a lack of understanding of the species abundances across archaeological sites, hindering interpretations of historical fisheries in the North Sea area. We use a new approach, utilising a combined 2D landmark-based geometric morphometric analysis as an objective and non-destructive method for species identification of flatfish vertebrae from the North Sea area. Modern specimens were used as a reference to describe the morphological variation between taxa using principal component analysis (PCA) and to trial an automated classification using linear discriminant analysis. Although there is limited distinction between taxa using PCAs, the classification shows high accuracies, indicating that flatfish species identifications using geometric morphometrics are possible. Bone samples (n = 105) from two archaeological sites in the United Kingdom and France were analysed using this approach and their identifications were verified using collagen peptide mass fingerprinting. The success rate of species identification was usually less than 50%, indicating that this technique has limited applicability due to preservation/fragmentation of archaeological fish bone. Nonetheless, this could prove a valuable tool for modern and non-fragmented samples. Furthermore, the technique applied in this study can be easily adapted to work on other landmark datasets.

Genome-Wide Identification of Aqp Family Related to Spermatogenesis in Turbot (Scophthalmus maximus).

The development and maturation of sperm entails intricate metabolic processes involving water molecules, amino acids, hormones, and various substances. Among these processes, the role of aquaporins (aqps) in the testis is crucial. Turbot (Scophthalmus maximus) is a significant marine flatfish species in China; however, natural egg laying in females is not feasible under cultured conditions. Consequently, artificial insemination becomes necessary, requiring the retrieval of sperm and eggs through artificial methods. In this study, we combined genomic, transcriptomics, RT-qPCR, computer-assisted sperm analysis (CASA), and immunohistochemistry to investigate the involvement of the aqp family in spermatogenesis in turbot. Through genomic data analysis, we identified 16 aqps genes dispersed across 13 chromosomes, each exhibiting the characteristic major intrinsic protein (MIP) domain associated with AQPs. The results from RNA-seq and RT-qPCR analysis revealed prominent expression of aqp4, 10, and 12 during the proliferative stage, whereas aqp1 showed primary expression during the mature stage. aqp11 displayed high expression levels during both MSII and MSV stages, potentially contributing significantly to the proliferation and maturation of male germ cells. Conversely, aqp8 showed elevated expression levels during the MSIII, MSIII-IV, and MSIV stages, suggesting its direct involvement in spermiogenesis. Immunohistochemical analysis unveiled the predominant localization of AQP1 protein in male germ cells rather than Sertoli cells, specifically concentrated in the head of sperm within cysts. Furthermore, a noteworthy decline in sperm motility was observed when sperm were subjected to treatment with either the AQP1-specific inhibitor (HgCl2) or the AQP1 antibody. However, no direct correlation was found between the expression of Smaqp1 and sperm quality. Overall, these findings provide new insights into the involvement of aqps in teleost spermatogenesis. Moreover, they hold potential for improving techniques related to sperm activation and cryopreservation, offering valuable knowledge for future advancements in this field.

Fast and user-friendly detection of flatfish species (Pleuronectes platessa and Solea solea) via Loop-Mediated Isothermal Amplification (LAMP)

Fast and user-friendly detection of flatfish species (Pleuronectes platessa and Solea solea) via Loop-Mediated Isothermal Amplification (LAMP)

Skeletal muscle growth activity of Olive Flounder (Paralichthys olivaceus) meat digest

Mammalian skeletal muscles play a pivotal role in the body and are mainly responsible for movement, metabolism, and energy consumption. Proteins that regulate muscle hypertrophy and atrophy are involved in muscle growth. A sufficient intake of dietary protein is essential for maintaining good health during normal growth and aging. Olive flounder (Paralichthys olivaceus) is one of the most common flatfish species in the South Korean aquaculture industry, and its consumption has been associated with various health benefits, such as a lower risk of cancers, heart failure, and chronic diseases. The present study attempted to determine the effect on muscle growth of flounder meat digest prepared using an in vitro gastric model. The capacity of digested flounder meat to enhance muscle growth was evaluated by examining glycogen levels and creatine kinase activity during muscle differentiation. The expression of muscle growth regulatory proteins was also evaluated. Treatment with flounder meat digest significantly and dose-dependently increased glycogen levels and creatine kinase activity in C2C12 cells. Moreover, proteins that are responsible for muscle hypertrophy and atrophy were significantly upregulated and downregulated, respectively. These results were confirmed using western blotting and immunofluorescence assays. The results of this study suggest that digested flounder meat has great potential for skeletal muscle growth and can be used as a functional food ingredient.

Contemporary analyses of comparative fishing data: a case study of Thorny skate on the Grand Banks (NAFO Divisions 3LNOP)

We re-analyze Thorny skate data from two comparative fishing experiments conducted by DFO in 1995 and 1996 using improved and more contemporary methods to estimate the relative efficiency of the Campelen 1800 demersal shrimp trawl survey protocol compared to the Engel 145 otter trawl. We correct possible bias in the method previously applied to these data. We investigate if there are size-based differences and if depth or spatial regions have important effects on results. We also investigate the influence and robustness of the estimation procedures, which was a concern in the original analyses of these data for other groundfish species. We did not find strong evidence that the relative efficiency of the Campelen trawl protocol compared to the Engel was different for smaller-sized Thorny skate compared to larger ones. However, we conclude that there is a potential that size-based differential catchability existed but there is insufficient information to reliably estimate these effects for Thorny skate. We also found evidence of significant differences in relative efficiency among NAFO Divisions and experiments, which is similar to other flatfish species. However, the mechanisms for these differences are unknown and it is not clear if spatial estimates should be used when converting Engel indices to Campelen equivalents. Hence, we do not recommend a different Engel-Campelen conversion factor than the one currently used in stock assessments for Thorny skates on the Grand Banks (NAFO Divisions 3LNOPs).

UK long-term monitoring dataset: assessing factors affecting biomarkers commonly used in environmental programmes

Long-term programmes like the UK Clean Seas Environmental Monitoring Programme (CSEMP) rely on biological effects techniques, including biomarkers, to assess if chemical pollutants are affecting sentinel species in the aquatic environment. In this study, we have applied mixed and fixed effect linear models to the long-term CSEMP dataset (2005-2018) to evaluate if factors such as region (location), sex, age, gonadosomatic index (GSI) and condition factor (CF), contribute to the variability observed in the levels of 3 well established biomarkers (inhibition of acetylcholinesterase in muscle-AChE, induction of hepatic 7-ethoxyresorufin-O-deethylase-EROD and presence of biliary 1-hydroxypyrene-1-OH pyrene) used to monitor biological effects of contaminants in dab (Limanda limanda) around UK waters. Regional differences (location) were a significant explanatory variable for the 3 biomarkers. Substantial differences were found in regional average muscle AChE activity, overall indicating the East Coast regions as likely more impacted by acetylcholinesterase inhibitors (e.g. organophosphates and carbamates). We report for the first time that, while accounting for region, sex and gonadosomatic index are significant predictors of muscle acetylcholinesterase isoform in dab (R2 = 0.13-0.15), and therefore advise the future analysis of this marker should be done by sex when reporting for marine environmental purposes. Dab condition factor is also a significant predictor for both enzymatic markers (AChE and EROD) but not for 1-OH pyrene. Sex and age, and their interaction, were the strongest variables (R2 = 0.46) influencing hepatic EROD, showing that although overall females had higher hepatic EROD, male dab hepatic EROD increased with age. Correlations between the three biomarkers might assist in discerning types of prevalent regional contamination over the studied period. Our results highlight the factors to account for when assessing if environmental contamination is contributing to the responses of these 3 biomarkers in dab, and other flatfish species, used in marine environmental monitoring programmes.

Correlations between oxidative DNA damage and formation of hepatic tumours in two flatfish species from contaminated environments.

Many species in aquatic environments face increased exposure to oncogenic pollution due to anthropogenic environmental change which can lead to higher cancer prevalence. The mechanistic relationship connecting environmental pollution and cancer is multi-factorial and poorly understood, and the specific mechanisms are so far still uncharacterized. One potential mediator between pollutant exposure and cancer is oxidative damage to DNA. We conducted a study in the field with two flatfish species, European flounder (Platichthys flesus L.) and common dab (Limanda limanda L.) with overlapping distribution and similar ecological niche, to investigate if the link between oncogenic pollutants and cancer described in ecotoxicological literature could be mediated by oxidative DNA damage. This was not the case for flounders as neither polycyclic aromatic hydrocarbon (PAH) bile metabolites nor metallic trace element concentrations were related to oxidative DNA damage measurements. However, dabs with higher PAH concentrations did exhibit increased oxidative damage. High oxidative DNA damage also did not predict neoplasm occurrence, rather, healthy individuals tended to have higher oxidative damage measurements compared to fishes with pre-neoplastic tumours. Our analyses showed that flounders had lower concentrations of PAH bile metabolites, suggesting that compared to dab this species is less exposed or better at eliminating these contaminants.

Detection and quantification of two commercial flatfishes (Solea solea and Pleuronectes platessa) in the North Sea using environmental DNA

AbstractSustainable fisheries management requires regular scientific monitoring of fish stocks. When information on certain fish stocks is limited, environmental DNA (eDNA) holds promise to complement traditional monitoring surveys. However, a better understanding of how eDNA concentrations relate to fish abundance and biomass is needed. Here, eDNA quantification of two commercially important flatfish species in the North‐East Atlantic, common sole (Solea solea) and European plaice (Pleuronectes platessa), was assessed. First, species‐specific, probe‐based assays for plaice and sole targeting the mitochondrial cytochrome b and cytochrome c oxidase subunit I gene, respectively, were developed (for sole) and validated (for both species). Subsequently, two mesocosm experiments revealed a significant and positive relationship between both abundance and biomass and eDNA concentrations for both species at three eDNA emission time periods (5 min, 1 h, and 24 h). Larger plaice shed significantly more eDNA (copies L−1) than smaller conspecifics. Finally, eDNA was obtained from seawater collected during research surveys in the Belgian part of the North Sea in spring 2020 (i.e., local scale) and the southwestern North Sea in autumn 2020 and 2021 (i.e., regional scale). eDNA concentrations were compared to the observed abundance (individuals per km2) and fish density in terms of biomass (kg per km2) as observed in the trawl at the same station. Local eDNA concentrations of both sole and plaice were positively correlated with observed abundance and fish density. The correlation between regional eDNA concentrations and fish density was positive and significant for sole in 2020 and 2021 and for plaice in 2020, but not in 2021. The correlation between regional eDNA concentrations and observed abundance was positive and significant for sole and plaice in 2020, but not in 2021. These results illustrate the potential of eDNA to estimate abundance and biomass parameters for stock assessments of flatfishes in the North Sea.

Correlations between oxidative DNA damage and formation of hepatic neoplasms in two flatfish species from contaminated environment

Correlations between oxidative DNA damage and formation of hepatic neoplasms in two flatfish species from contaminated environment

Correlations between oxidative DNA damage and formation of hepatic neoplasms in two flatfish species from contaminated environment

Correlations between oxidative DNA damage and formation of hepatic neoplasms in two flatfish species from contaminated environment

Genome-wide chromatin accessibility and gene expression profiling during flatfish metamorphosis

Metamorphosis is a widely studied post-embryonic process in which many tissues undergo dramatic modifications to adapt to the new adult lifestyle. Flatfishes represent a good example of metamorphosis in teleost fishes. During metamorphosis of flatfish, organ regression and neoformation occur, with one of the most notable changes being the migration of one of the eyes to the other side of the body. In order to create a useful and reliable tool to advance the molecular study of metamorphosis in flatfish, we generated a chromatin accessible atlas as well as gene expression profile during four developmental stages ranging from a phylotypic to a post-metamorphic stage. We identified 29,019 differentially accessible chromatin regions and 3,253 differentially expressed genes. We found stage-specific regulatory regions and gene expression profiles, supporting the quality of the results. Our work provides strongly reproducible data for further studies to elucidate the regulatory elements that ensure successful metamorphosis in flatfish species.

Every animal matters! Evaluating the selectivity of a Mediterranean bottom trawl fishery from a species community perspective.

Bottom trawl fisheries often catch several species simultaneously. However, most studies addressing the catch performance and selectivity of a specific trawl focus on a few commercially important or most vulnerable species requiring management measures. By contrast, the present study considers the multispecies nature of Mediterranean bottom trawl fisheries through a holistic approach that accounts for the full species community in the catches. Specifically, we evaluated and compared the catch performance of the two codends allowed for this fishery, made of 40 mm square (SM40) and 50 mm diamond (DM50) meshes. Results showed that 50 and 80% of the catch in weight and count numbers, respectively, consisted of species without commercial value, demonstrating that large proportions of the catch are not considered when using the existing approach to evaluate the ecological impact of the fishing activity. Significant differences in catch profiles between the two codends were observed, especially for two commercial flatfish species, Arnoglossus laterna and Citharus linguatula, with larger contributions in the SM40. Further, the SM40 codend had a significantly higher retention, compared to DM50 codend, for specific sizes of Merluccius merluccius and Mullus barbatus. The outcomes of the study can be useful for the Mediterranean bottom trawl fisheries management.

Testing of a helix twine off-bottom trawl on Georges Bank

The massive biomass of Eastern Georges Bank haddock (Melanogrammus aeglefinus) is difficult to harvest without capturing less robust, but still valuable groundfish stocks like Atlantic cod (Gadus morhua) and some flatfish species. Specialized haddock trawls that raise the mouth of the nets off-bottom have reduced bycatch but the very poor status of Atlantic cod prioritizes even greater reduction to prevent exceeding regulatory fishing quotas. Raising the entire fishing gear off-bottom may further reduce bycatch while eliminating benthic impacts, expanding access to grounds previously off-limits to bottom-tending trawls. We evaluated an off-bottom trawl (OBT) to harvest Eastern Georges Bank haddock while reducing catches of overexploited stocks. The OBT net has very large meshes at the front end, made with innovative “helix” twine that produces lateral hydraulic forces while towing, resulting in self-spreading of the meshes. We established optimal gear configurations to achieve the target OBT net shape and distance to the seafloor by using an assortment of mensuration sensors/loggers and cameras. The OBT caught similar amounts of haddock and reduced some bycatch more than a standard bottom “Ruhle trawl”, but also caught fish of the same lengths despite the OBT using a smaller mesh-sized codend. The OBT also demonstrated similar requirements in vessel RPMs as the Ruhle trawl, despite having a larger swept area.

A new concept for bycatch reduction in small-scale accordion-shaped trap fisheries of the Yellow Sea, China

The bycatch issue is a major concern in small-scale accordion-shaped trap fisheries in the Yellow Sea of China because of the poor species and size selectivity of fishing gear and the co-occurrence of multispecies. Two threatened flatfish species assessed by the IUCN, marbled flounder (Pseudopleuronectes yokohamae) and stone flounder (Platichthys bicoloratus), are the two main bycatches in accordion-shaped trap fisheries. This fishery also captures a large proportion of juvenile target species, resulting in both recruitment and growth overfishing of these species. In this study, we introduced a new concept of a combined sorting grid and escape vent (CSEV), a selection device aimed at reducing the bycatch of flatfish and undersized target species in mixed-species trap fisheries. We used a catch comparison method to assess the performance of the CSEV in field experiments, with conventional traps as the baseline. Our results demonstrated that the CSEV significantly improved the species and size selectivity of the traps. Test traps mounted with the CSEV significantly reduced the catch rates of marbled flounder and stone flounder by 70% and 74% throughout the length class, respectively, compared with conventional traps. The catch of undersized target species, namely, fat greenling (Hexagrammos otakii), black rockfish (Sebastes schlegelii), and Asian paddle crab (Charybdis japonica), was reduced by 79%, 75%, and 80%, respectively, while the catch rates of target-sized individuals were maintained or even improved. Given these promising results, the CSEV may have great potential for application in accordion-shaped trap fisheries and similar fisheries.

The Use of Sand Substrate Modulates Dominance Behaviour and Brain Gene Expression in a Flatfish Species

Physical complexity adds physical enrichment to rearing conditions. This enrichment promotes fish welfare and reduces detrimental characteristics that fish develop in captivity. Senegalese sole (Solea senegalensis) is an important species for European aquaculture, where it is reared in intensive conditions using fibreglass tanks. However, reproductive dysfunctions present in this species do not allow it to complete its life cycle in captivity. Recently, dominance behaviour has been studied to try to solve this problem. The present study aimed to assess the effect of sand as environmental enrichment in the dominance behaviour and brain mRNA abundance of Senegalese sole juveniles. Four tanks of sole (n = 48 fish in total) were established in two different environments (with and without sand). Juveniles were subjected to dominance tests of feeding and territoriality. Behaviours analysed by video recordings related to the distance from the food delivered and harassment behaviour towards other individuals (e.g., resting of the head on another individual). In both environments, dominant sole were the first to feed, displayed more head-resting behaviour and dominated the area close to the feeding point, where the events were reduced in fish maintained in the sand. mRNA expression related to differentiation of dopamine neurons (nr4a2) and regulation of maturation (fshra) were significantly upregulated in dominant fish in the sand environment compared to dominants maintained without sand. The use of an enriched environment may affect Senegalese sole dominance, enhance welfare and possibly advance future maturation.

The consequences of density‐dependent individual growth for sustainable harvesting and management of fish stocks

AbstractDensity dependence is likely to act as a regulatory mechanism in fish stocks that are recovering from overfishing. In general, density dependence in fish stocks is assumed to only occur in reproduction and early life stages and is therefore usually modelled as a stock‐recruitment relationship. Recent research shows that density dependence can also reduce individual growth in body size later in life. In this study, we show how optimal fishing effort changes with the strength of density dependence in individual growth for four stocks of North Sea flatfish species. Using size‐structured population models we show that density dependence arises due to a mechanistic link between the resource availability and life history processes at the individual level. We furthermore show that the stock response to harvesting is either driven by changes in individual reproduction when density dependence in individual growth is weak or by changes in individual growth rate when individual growth is strongly affected by density dependence. These two types or regimes are separated by a sudden shift in dynamics. It is therefore of great importance to account for density dependence in growth when managing fish stocks.