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Global change stressors can modify ecological niches of species, thereby altering ecological interactions within communities and food webs. Yet, some species might take advantage of a fast‐changing environment, allowing species with high niche plasticity to thrive under climate change. We used natural CO2 vents to test the effects of ocean acidification on niche modifications of a temperate rocky reef fish assemblage. We quantified three ecological niche traits (overlap, shift and breadth) across three key niche dimensions (trophic, habitat and behavioural). Only one species increased its niche width along multiple niche dimensions (trophic and behavioural), shifted its niche in the remaining (habitat) was the only species to experience a highly increased density (i.e. doubling) at vents. The other three species that showed slightly increased or declining densities at vents only displayed a niche width increase in one (habitat niche) out of seven niche metrics considered. This niche modification was likely in response to habitat simplification (transition to a system dominated by turf algae) under ocean acidification. We further showed that, at the vents, the less abundant fishes had a negligible competitive impact on the most abundant and common species. This species appeared to expand its niche space, overlapping with other species, which likely led to lower abundances of the latter under elevated CO2. We conclude that niche plasticity across multiple dimensions could be a potential adaptation in fishes to benefit from a changing environment in a high‐CO2 world. [ABSTRACT FROM AUTHOR]

Oogenesis has universal characteristics among fishes, in which structures of vital importance for embryos are assembled. However, these universal structures may have additional functions depending on the evolutionary ecology of each species. The aim of this research was to describe histologically the structure of the ovary and the oogenesis of the pupfishes Cyprinodon artifrons and Garmanella pulchra, with emphasis on the follicular structures linked to the resistance of embryos to desiccation. The embryos of pupfishes experience periodic deleterious environmental changes caused by estuarine tides. They can survive periods out of water protected by accessory egg layers assembled in the ovaries during oogenesis. This research found that both species have a single ovary with asynchronous follicle development, associated with a frequent breeding activity. Also, multiple generations of cortical alveoli were described, larger in G. pulchra, related with the formation of perivitelline space, a structure that can buffer the effects of desiccation when embryos remain out of water. In both species, the accumulation of oil droplets in the oocytes was simultaneous with the synthesis of cortical alveoli. Oil droplets may be related to energy reserves during extended incubation periods. The zona pellucida of both species presented an intermediate thickness with respect to other species, and hair-like filaments arranged on the zona pellucida of G. pulchra were clearly detected. These structures as a whole, could be related to the survival of the embryos of the pupfishes of Yucatan in the tidal fluctuations in the estuarine environments in which they inhabit. [ABSTRACT FROM AUTHOR]

Abyssal (3501–6500 m) and hadal (>6500 m) fauna evolve under harsh abiotic stresses, characterized by high hydrostatic pressure, darkness and food shortage, providing unique opportunities to investigate mechanisms underlying environmental adaptation. Genomes of several hadal species have recently been reported. However, the genetic adaptation of deep sea species across a broad spectrum of ocean depths has yet to be thoroughly investigated, due to the challenges imposed by collecting the deep sea species. To elucidate the correlation between genetic innovation and vertical distribution, we generated a chromosome‐level genome assembly of the macrourids Coryphaenoides yaquinae, which is widely distributed in the abyssal/hadal zone ranging from 3655 to 7259 m in depth. Genomic comparisons among shallow, abyssal and hadal‐living species identified idiosyncratic and convergent genetic alterations underlying the extraordinary adaptations of deep‐sea species including light perception, circadian regulation, hydrostatic pressure and hunger tolerance. The deep‐sea fishes (Coryphaenoides Sp. and Pseudoliparis swirei) venturing into various ocean depths independently have undergone convergent amino acid substitutions in multiple proteins such as rhodopsin 1, pancreatic and duodenal homeobox 1 and melanocortin 4 receptor which are known or verified in zebrafish to be related with vision adaptation and energy expenditure. Convergent evolution events were also identified in heat shock protein 90 beta family member 1 and valosin‐containing protein genes known to be related to hydrostatic pressure adaptation specifically in fishes found around the hadal range. The uncovering of the molecular convergence among the deep‐sea species shed new light on the common genetic innovations required for deep‐sea adaptation by the fishes. [ABSTRACT FROM AUTHOR]

Exploring the effects of seasonal variation on the gut microbiota of cold-water fish plays an important role in understanding the relationship between seasonal variation and cold-water fish. Gut samples of cold-water fish and environmental samples were collected during summer and winter from the lower reaches of the Yalong River. The results of the 16S rRNA sequencing showed that significant differences were identified in the composition and diversity of gut bacteria of cold-water fish. Co-occurrence network complexity of the gut bacteria of cold-water fish was higher in summer compared to winter (Sum: nodes: 256; edges: 20,450; Win: nodes: 580; edges: 16,725). Furthermore, from summer to winter, the contribution of sediment bacteria (Sum: 5.3%;Win: 23.7%) decreased in the gut bacteria of cold-water fish, while the contribution of water bacteria (Sum: 0%; Win: 27.7%) increased. The normalized stochastic ratio (NST) and infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP) showed that deterministic processes played a more important role than stochastic processes in the microbial assembly mechanism of gut bacteria of cold-water fish. From summer to winter, the contribution of deterministic processes to gut bacteria community assembly mechanisms decreased, while the contribution of stochastic processes increased. Overall, these results demonstrated that seasonal variation influenced the gut bacteria of cold-water fish and served as a potential reference for future research to understand the adaptation of fish to varying environments. [ABSTRACT FROM AUTHOR]

Vibrio harveyi is a normal flora in natural marine habitats and a significant opportunistic pathogen in marine animals. This bacterium can cause a series of lesions after infecting marine animals, in which muscle necrosis and ulcers are the most common symptoms. This study explored the adaptation mechanisms of V. harveyi from the seawater environment to host fish muscle environment. The comprehensive transcriptome analysis revealed dramatic changes in the transcriptome of V. harveyi during its adaptation to the host fish muscle environment. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, flagellar assembly, oxidative phosphorylation, bacterial chemotaxis, and two-component systems play crucial roles in V. harveyi's adaptation to host fish muscle. A comparison of biological phenotypes revealed that V. harveyi displayed a significant increase in flagellar length, swimming, twitching, chemotaxis, adhesion, and biofilm formation after induction by host fish muscle, and its dominant amino acids, especially bacterial chemotaxis induced by host muscle, Ala and Arg. It could be speculated that the enhancement of bacterial chemotaxis induced by amino acids plays a key role in the adaptation of V. harveyi from seawater to the muscle of the host fish. [ABSTRACT FROM AUTHOR]

Aquaculture is considered one of the fastest-growing food production sectors, which provides about 41% of the world's fish food. Different types of pathogens, including bacteria, viruses, amoebas, oomycetes, fungi, and ectoparasites, have emerged to cause serious fish diseases. Medicines such as antibiotics and chemicals as well as vaccines have been widely used to combat fish diseases. However, their undesirable use to treat fish in aquaculture develops drug resistance in the surrounding microbes, especially antibiotic resistance in fish-associated bacterial strains in the column water and sediment, is mostly the consequence of applying antibiotics in aquaculture. The rise of antibiotic resistance in aquaculture and multidrug-resistant pathogens in the food chain threatens public health, hampering infection treatment and compromising food safety. Addressing this challenge is vital to protect both public well-being and the aquaculture industry's future. Basic control measures for sustainable, disease-free aquaculture, including alteration of antibiotic resistance genes into other animal pathogens, have been driven by the potential development of antibiotics with respect to environmental impact and consumer safety. Anyhow, vaccination is an effective control measure that overcomes drug resistance conditions in aquaculture; even some therapeutic and prophylactic methods are being simultaneously applied for the treatment of fish diseases. Mostly, antibiotics and probiotics do not show strong effects after the development of new mutant strains and drug-resistant pathogens. Therefore, various types of vaccines have been developed to treat aquatic pathogens effectively by using advanced molecular techniques. Previous studies on fish vaccines have typically lacked comprehensive assessments of vaccine efficacy across varying environments and species, often focusing on single pathogens while neglecting the potential influence of pathogen interactions within complex aquatic ecosystems. This review focuses on advancements in technology and prospects of vaccines used in the aquaculture industries for reducing antibiotics usage. It also discussed the vaccination from traditional to modern new-generation ones including DNA, monovalent, and polyvalent vaccines. The objective is to provide an overview of aquaculture's major bacterial pathogens and how vaccines can substitute antibiotics to protect aquatic animals from various infectious diseases. [ABSTRACT FROM AUTHOR]

Background: Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited. Results: A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome. Conclusions: We have assembled and annotated the Patagonian toothfish genome, which will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species. [ABSTRACT FROM AUTHOR]

Background: Fish scales are typical products of biomineralization and play an important role in the adaptation of fish to their environment. The Gymnocypris przewalskii scales are highly specialized, with scales embedded in only specific parts of the dermis, such as the areas around the anal fin and branchiostegite, making G. przewalskii an ideal material for biomineralization research. In this study, we aimed to unveil genes and pathways controlling scale formation through an integrated analysis of both transcriptome and proteome, of which G. przewalskii tissues of the dorsal skin (no scales) and the rump side skin (with scales) were sequenced. The sequencing results were further combined with cellular experiments to clarify the relationship between genes and signaling pathways. Results: The results indicated the following: (1) a total of 4,904 differentially expressed genes were screened out, including 3,294 upregulated genes and 1,610 downregulated genes (with a filtering threshold of |log2Fold-Change|> 1 and p-adjust < 0.05). The identified differentially expressed genes contained family members such as FGF, EDAR, Wnt10, and bmp. (2) A total of 535 differentially expressed proteins (DEPs) were filtered out from the proteome, with 204 DEPs downregulated and 331 DEPs upregulated (with a filtering threshold of |Fold-Change|> 1.5 and p < 0.05). (3) Integrated analyses of transcriptome and proteome revealed that emefp1, col1a1, col6a2, col16a1, krt8, and krt18 were important genes contributing to scale development and that PI3K-AKT was the most important signaling pathway involved. (4) With the use of the constructed G. przewalskii fibroblast cell line, emefp1, col1a1, col6a2, col16a1, krt8, and krt18 were confirmed to be positively regulated by the PI3K-AKT signaling pathway. Conclusion: This study provides experimental evidence for PI3K-AKT controlled scale development in G. przewalskii and would benefit further study on stress adaptation, scale biomineralization, and the development of skin appendages. [ABSTRACT FROM AUTHOR]

The European Fish Index EFI+ is the only fish-based multimetric index for the assessment of the ecological status of running waters that is validated and thus applicable across most countries of the European Union. Metrics of the index rely on several attributes of the species present in the fish assemblage, irrespective of their native/alien status. The abundance of alien fish, together with other anthropogenic impacts, is one of the most important threats to the conservation of native fish and ecosystem health and is also an indicator of degraded stream conditions. Therefore, to improve the performance of the EFI+ in regions with high incidence of alien species, the EFI+ was adapted to include alien fish pressure as a new metric that reflects the number of alien species as well as the proportional abundance of alien individuals. The application of the adapted index (A-EFI+) is illustrated with data from several Iberian Mediterranean basins and showed similar or stronger correlations than the original EFI+ with anthropogenic pressure (land-use variables and alterations in hydrology and river morphology) and with other regional fish indices. EFI+ has been invaluable to intercalibrate fish indices across Europe, and A-EFI+ is similar but explicitly includes alien pressure, thus helping to provide a more comprehensive assessment of ecosystem health and to communicate it to society. [ABSTRACT FROM AUTHOR]

The schizothoracine fishes, widely distributed in the Qinghai-Tibetan Plateau and its adjacent areas, are considered as ideal models for investigation of high-altitude adaptation. Schizophygopsis are one group of the highly specialized schizothoracine fishes, and the genetic basis for their high-altitude adaptation is poorly understood. In this study, we performed comparative genomics analyses to investigate the potential genetic mechanisms for high-altitude adaptation of Schizopygopsis malacanthus and Schizopygopsis pylzovi based on the chromosome-level genomes. Functional enrichment analysis revealed that many expanded gene families in Schizopygopsis were associated with immune response while many contracted gene families were functionally associated with olfaction. Among the 123 positively selected genes (PSGs), angpt2a was detected in HIF-1 signaling pathway and possibly related to the hypoxia adaptation of Schizopygopsis. Furthermore, two PSGs cox15 and ndufb10 were distributed in thermogenesis, and there was a Schizopygopsis -specific missense mutation in cox15 (Gln115Glu), which possibly contributed to the cold temperature adaptation of the Schizopygopsis. Kyoto Encyclopedia of Genes and Genomes enrichment of the PSGs revealed three significant pathways including metabolic pathways, cell cycle, and homologous recombination and Gene Ontology enrichment analysis of the PSGs revealed several categories associated with DNA repair, cellular response to DNA damage stimulus, and metabolic process. Chromosome-scale characterization of olfactory receptor (OR) repertoires indicated that Schizopygopsis had the least number of OR genes, and the OR gene contraction was possibly caused by the limited food variety and the environmental factors such as lower air pressure, lower humidity, and lower temperature. Our study will help expand our understanding of the potential adaptive mechanism of Schizopygopsis to cope with the high-altitude conditions. [ABSTRACT FROM AUTHOR]

The bacterium strain Cetobacterium sp. C33 was isolated from the intestinal microbial content of Nile tilapia (O. niloticus) under anaerobic conditions. Given that Cetobacterium species are recognized as primary constituents of the intestinal microbiota in cultured Nile tilapia by culture-independent techniques, the adaptability of the C33 strain to the host gastrointestinal conditions, its antibacterial activity against aquaculture bacterial and its antibiotic susceptibility were assessed. The genome of C33 was sequenced, assembled, annotated, and subjected to functional inference, particularly regarding pinpointed probiotic activities. Furthermore, phylogenomic comparative analyses were performed including closely reported strains/species relatives. Comparative genomics with closely related species disclosed that the isolate is not phylogenetically identical to other Cetobacterium species, displaying an approximately 5% sequence divergence from C. somerae and a 13% sequence divergence from Cetobacterium ceti. It can be distinguished from other species through physiological and biochemical criteria. Whole-genome annotation highlighted that Cetobacterium sp. nov. C33 possesses a set of genes that may contribute to antagonism against competing bacteria and has specific symbiotic adaptations in fish. Additional in vivo experiments should be carried out to verify favorable features, reinforcing its potential as a probiotic bacterium. [ABSTRACT FROM AUTHOR]

Nitrite toxicity poses a significant threat to aquatic organisms, including largemouth bass (LMB) and Micropterus salmoides. This study aimed to elucidate the role of bZIP transcription factors in mediating the molecular responses to nitrite stress in the LMB spleen. We identified 120 bZIP genes in the LMB genome using bioinformatics analysis and divided them into 11 subgroups based on phylogenetic relationships. Under nitrite stress, the bZIP_XI subgroup was upregulated, suggesting the activation of the stress response in the LMB spleen. Cellular pathway analysis revealed enrichment of pathways related to stress response, DNA repair, apoptosis, and autophagy. Co-expression network analysis highlighted bZIP_XI members such as msabZIP_49, msabZIP_12, msabZIP_39, and msabZIP_116 as potential key regulators. These transcription factors likely modulated the expression of stress-related genes like VCAM1, POLE3, and BMP1. Conserved binding motifs in the promoters of these genes may support regulation by bZIP_XI. Furthermore, bZIP_XI members correlated with immune cell infiltration in the spleen, potentially regulating immune-related genes like BCL2L1 and SELE. Homologs of bZIP_XI in other fish species exhibited similar expression patterns under stress. Overall, this study implicates the bZIP transcription factor family, notably the bZIP_XI subgroup, in orchestrating the molecular response of the LMB spleen to nitrite toxicity by regulating stress response pathways and immune function. These findings provide insights into nitrite stress adaptation in fish. [ABSTRACT FROM AUTHOR]

The present study deals with the topography of retinal ganglion cells (GCs) and spatial resolution in the smelt Hypomesus japonicus. The eyes and retinae were examined by light microscopy and computerized tomography. DAPI labelling was used to visualize cell nuclei in the ganglion cell and inner plexiform layers. Two zones of increased GC density in the nasal and temporal retina were bridged by a horizontal streak with the GC density ranging from 5600 to 8000 cells/mm2. The maximum cell density (area retinae temporalis) ranged from 9492 to 14,112 cells/mm2, and the total number of GCs varied from 286 x 103 to 326 x 103 cells in three individuals. The theoretical anatomical spatial resolution (the anatomical estimate of the upper limit of visual acuity) was minimum in the ventral periphery (smaller fish, 1.43 cpd; larger fish, 1.37 cpd) and maximum in area retinae temporalis (smaller fish, 2.83 cpd; larger fish, 2.41 cpd). The relatively high density of GCs and presence of the horizontal streak and area retinae temporalis in the H. japonicus are consistent with its highly visual behaviour. The present findings contribute to better understanding of the factors affecting the topography of retinal ganglion cells and mechanisms of visual adaptation in fish. [ABSTRACT FROM AUTHOR]

The streams draining volcanic landscapes are often characterized by a complex series of factors that negatively affect hydrobionts and lead to declines in their populations. However, in a number of cases, a range of rapid adaptive changes ensure the resilience of hydrobiont populations. Here, we present both field and experimental data shedding light on the physiological basis of adaptation to heavy metal contamination in populations of Dolly Varden charr (Salvelinus malma) differing in duration of isolation in volcanic streams. The study reveals that isolated populations have a physiological phenotype that distinguishes them from populations inhabiting clean waters. They are characterized by a hyperthyroid status accompanied by an increased metabolic rate, elevated activity of antioxidant enzymes, decreased ionic conductivity of tissues and reduced stored energy reserves. Our experimental data reveal that hyperthyroidism is an adaptive characteristic enhancing the resistance to heavy metal contamination and shaping the evolution of these populations. The similarity of physiological, developmental and morphological changes in isolated populations suggests a common source and mechanisms underpinning this case of 'evolutionary rescue'. Thus, populations of S. malma trapped in volcanic streams represent a genuine case of rapid endocrine‐driven adaptation to changing environmental stimuli. [ABSTRACT FROM AUTHOR]

Communities along Canada's three coastlines heavily rely on the $3,500 million marine aquaculture and fishery sectors, but the changing climate threatens their viability, making adaptation to climate change in fisheries increasingly critical in the international setup. As ocean conditions are expected to undergo dramatic shifts, including significant changes in sea surface temperatures, ocean acidification levels, ocean currents, weather patterns, and overall ecosystem dynamics, proactive measures are essential to address the impacts on fish populations, marine resource sustainability, and the livelihoods of coastal communities. This study aims to investigate the relationship between fishing and climate velocity, specifically focusing on its effects on marine fish abundance and distribution. Simultaneously, it seeks to understand how fishers and fishing communities adapt to variations in species ranges while identifying incentives that promote the sustainability of marine life and economic stability in the context of climate change. To address these questions, we conducted a systematic review of existing research published between 2012 and 2022, spanning multiple databases, including the ACM Digital Library, PubMed, Google Scholar, Scopus, IEEE Xplore, and Web of Science. Out of a total of 4956 studies identified, 23 studies meeting predetermined inclusion criteria were selected. Our analysis uncovered a strong correlation between climate change and habitat modification, significantly impacting multiple fish species. Furthermore, our findings revealed that these risks have direct consequences on fish distribution, as well as on the angling industry and the communities that rely on it. By examining this extensive literature, we aimed to gain valuable insights, identify trends, and uncover any knowledge gaps related to fish distribution and abundance in Canada's waters, with the hope of informing policies and strategies that can help safeguard the future of these vital industries and the communities they support in the face of ongoing climate change.

The anti-protease inhibitory ability of the cestode Triaenophorus nodulosus (Pallas, 1781) was studied in extracts of its plerocercoid larvae from the liver of a perch (Perca fluviatilis Linnaeus) and in excretory-secretory products and extracts of its mature and immature forms from the intestine of a pike (Esox lucius Linnaeus). It was found that excretory/secretory products (ESP) and extracts of both mature and immature T. nodulosus exhibited varying degrees of anti-protease inhibitory ability, including toward commercial trypsin. Tapeworm extracts had a greater inhibitory ability compared to ESP. At the same time, the extract of immature tapeworms exhibited a higher anti-protease activity compared to mature forms. Likewise, the extract of tapeworms deprived of the brush border had a higher inhibitory ability compared to the tegumental brush border fraction. [ABSTRACT FROM AUTHOR]

Amazonian blackwaters are extremely biodiverse systems containing some of Earth's most naturally acidic, dissolved organic carbon -rich and ion‐poor waters. Physiological adaptations of fish facing these ionoregulatory challenges are unresolved but could involve microbially-mediated processes. Here, we characterize the physiological response of 964 fish-microbe systems from four blackwater Teleost species along a natural hydrochemical gradient, using dual RNA-Seq and 16 S rRNA of gill samples. We find that host transcriptional responses to blackwaters are species-specific, but occasionally include the overexpression of Toll-receptors and integrins associated to interkingdom communication. Blackwater gill microbiomes are characterized by a transcriptionally-active betaproteobacterial cluster potentially interfering with epithelial permeability. We explore further blackwater fish-microbe interactions by analyzing transcriptomes of axenic zebrafish larvae exposed to sterile, non-sterile and inverted (non-native bacterioplankton) blackwater. We find that axenic zebrafish survive poorly when exposed to sterile/inverted blackwater. Overall, our results suggest a critical role for endogenous symbionts in blackwater fish physiology. Amazonian blackwaters are acidic and physiologically-challenging, but are one of Earth's most diversified ecosystems. This study revealed that fish survival in these hostile habitats depends on the colonization of their gills by endogenous blackwater Betaproteobacteria, with the potential to regulate host ionoregulatory processes. [ABSTRACT FROM AUTHOR]

Simple Summary: The reduction in seawater pH as a consequence of ocean acidification has resulted in a considerable challenge for the adaptation of fish. The effects of pH fluctuations in coastal regions on offshore fish are not fully understood in terms of their behavioral and physiological responses. In the present study, we aimed to examine the consequences of a brief period of reduced pH levels on the behavioral and physiological performance of juvenile black rockfish (Sebastes schlegelii). The findings revealed that juvenile black rockfish could withstand changes in pH, but there was a significant impact on their activity state and metabolic levels. The present study will enhance our understanding of the behavioral and physiological responses of costal fish (the black rockfish, in this case) to acidic conditions. Coastal areas are subject to greater pH fluctuation and more rapid pH decline as a result of both natural and anthropogenic influences in contrast to open ocean environments. Such variations in pH have the potential to pose a threat to the survival and physiological function of offshore fishes. With the aim of evaluating the impact of short-term pH reduction on the behavioral performance and physiological response of costal fish, the black rockfish (Sebastes schlegelii), one of the principal stock-enhanced species, was examined. In the present study, juveniles of the black rockfish with a mean body length of 6.9 ± 0.3 cm and weight of 8.5 ± 0.5 g were exposed to a series of pHs, 7.0, 7.2, 7.4, 7.6, 7.8, and normal seawater (pH 8.0) for 96 h. At the predetermined time points post-exposure (i.e., 0, 12, 24, 48, and 96 h), fish movement behavior was recorded and the specimens were sampled to assess their physiological responses. The results indicate that the lowered pH environment (pH 7.0–7.8) elicited a significant increase in highly mobile behavior, a decrease in immobile behavior, and a significant rise in the metabolic levels of the black rockfish juveniles. Specifically, carbohydrate metabolism was significantly elevated in the pH 7.2 and 7.4 treatments, while lipid metabolism was significantly increased in the pH 7.0, 7.4, and 7.8 treatments. The results of the present study indicate that short-term reductions in pH could ramp up boldness and boost energy expenditure in the black rockfish juveniles, leading to an increased metabolic cost. Additionally, the present investigation revealed that the black rockfish juveniles were capable of adapting to a short-term pH reduction. The findings may provide insight into the underlying physiological mechanisms that govern fish responses to potential decreases in seawater pH in the future. [ABSTRACT FROM AUTHOR]

Host-microbiota interactions play critical roles in host development, immunity, metabolism, and behavior. However, information regarding host-microbiota interactions is limited in fishes due to their complex living environment. In the present study, an allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) was used to investigate the successional changes of the microbial communities and host-microbiota interactions during herbivorous and carnivorous dietary adaptations. The growth level was not significantly different in any developmental stage between the two diet groups of fish. The diversity and composition of the dominant microbial communities showed similar successional patterns in the early developmental stages, but significantly changed during the two dietary adaptations. A large number of bacterial communities coexisted in all developmental stages, whereas the abundance of some genera associated with metabolism, including Acinetobacter, Gemmobacter, Microbacterium, Vibrio, and Aeromonas, was higher in either diet groups of fish. Moreover, the abundance of phylum Firmicutes, Actinobacteria, and Chloroflexi was positively correlated with the host growth level. In addition, Spearman's correlation analysis revealed that the differentially expressed homologous genes in the intestine associated with cell growth, immunity, and metabolism were related to the dominant gut microbiota. Our results present evidence that host genetics-gut microbiota interactions contribute to dietary adaptation in hybrid fish, which also provides basic data for understanding the diversity of dietary adaptations and evolution in fish. [ABSTRACT FROM AUTHOR]

Simple Summary: Hypoxic stress often occurs in aquaculture environments and is primarily mediated by the hypoxia-inducible factor 1 (HIF-1) signaling pathway. Prolyl hydroxylase domain proteins (PHD) are cellular oxygen-sensing molecules that regulate the stability of HIF-1α. In this study, the characterization of the PHD2 from mandarin fish Siniperca chuatsi (scPHD2) and its roles in the HIF-1 signaling pathway were investigated. This study furthers our understanding of the molecular mechanisms underlying hypoxia adaptation in teleost fish. With increased breeding density, the phenomenon of hypoxia gradually increases in aquaculture. Hypoxia is primarily mediated by the hypoxia-inducible factor 1 (HIF-1) signaling pathway. Prolyl hydroxylase domain proteins (PHD) are cellular oxygen-sensing molecules that regulate the stability of HIF-1α through hydroxylation. In this study, the characterization of the PHD2 from mandarin fish Siniperca chuatsi (scPHD2) and its roles in the HIF-1 signaling pathway were investigated. Bioinformation analysis showed that scPHD2 had the conserved prolyl 4-hydroxylase alpha subunit homolog domains at its C-terminal and was more closely related to other Perciformes PHD2 than other PHD2. Tissue-distribution results revealed that scphd2 gene was expressed in all tissues tested and more highly expressed in blood and liver than in other tested tissues. Dual-luciferase reporter gene and RT-qPCR assays showed that scPHD2 overexpression could significantly inhibit the HIF-1 signaling pathway. Co-immunoprecipitation analysis showed that scPHD2 could interact with scHIF-1α. Protein degradation experiment results suggested that scPHD2 could promote scHIF-1α degradation through the proteasome degradation pathway. This study advances our understanding of how the HIF-1 signaling pathway is regulated by scPHD2 and will help in understanding the molecular mechanisms underlying hypoxia adaptation in teleost fish. [ABSTRACT FROM AUTHOR]

Simple Summary: The liver transcriptome was analyzed after 22 d culture with different salinity water using RNA sequencing (RNA-seq) in spotted scat (Scatophagus argus). The genes involved in lipid metabolism were differentially down- or up-regulated in low (5 ppt)- and high (35 ppt)-salinity-rated fish in comparison with the control (25 ppt) group. The difference in liver lipid metabolism is important to adapt to low- and high-salinity stress in spotted scat, which has an important value for understanding the molecular basis of salinity adaptation in euryhaline fish. Spotted scat (Scatophagus argus) can tolerate a wide range of salinity fluctuations. It is a good model for studying environmental salinity adaptation. Lipid metabolism plays an important role in salinity adaptation in fish. To elucidate the mechanism of lipid metabolism in the osmoregulation, the liver transcriptome was analyzed after 22 d culture with a salinity of 5 ppt (Low-salinity group: LS), 25 ppt (Control group: Ctrl), and 35 ppt (High-salinity group: HS) water by using RNA sequencing (RNA-seq) in spotted scat. RNA-seq analysis showed that 1276 and 2768 differentially expressed genes (DEGs) were identified in the LS vs. Ctrl and HS vs. Ctrl, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the pathways of steroid hormone biosynthesis, steroid biosynthesis, glycerophospholipid metabolism, glycerolipid metabolism, and lipid metabolism were significantly enriched in the LS vs. Ctrl. The genes of steroid biosynthesis (sqle, dhcr7, and cyp51a1), steroid hormone biosynthesis (ugt2a1, ugt2a2, ugt2b20, and ugt2b31), and glycerophospholipid metabolism (cept1, pla2g4a, and ptdss2) were significantly down-regulated in the LS vs. Ctrl. The pathways related to lipid metabolisms, such as fatty acid metabolism, fatty acid biosynthesis, peroxisome proliferator-activated receptor (PPAR) signaling pathway, adipocytokine signaling pathway, fatty acid degradation, and unsaturated fatty acid biosynthesis, were significantly enriched in the HS vs. Ctrl. The genes of unsaturated fatty acid biosynthesis (scd1, hacd3, fads2, pecr, and elovl1) and adipocytokine signaling pathway (g6pc1, socs1, socs3, adipor2, pck1, and pparα) were significantly up-regulated in the HS vs. Ctrl. These results suggest that the difference in liver lipid metabolism is important to adapt to low- and high-salinity stress in spotted scat, which clarifies the molecular regulatory mechanisms of salinity adaptation in euryhaline fish. [ABSTRACT FROM AUTHOR]

Cold-adapted enzymes from psychrophilic and psychrotolerant species are characterized by a higher catalytic activity at low temperature than their mesophilic orthologs and are also usually found to be more thermolabile. Computer simulations of the catalytic reactions have been shown to be a very powerful tool for analyzing the structural and energetic origins of these effects. Here, we examine the cold adaptation of lactate dehydrogenases from two Antarctic and sub-Antarctic fish species using this approach and compare our results with those obtained for the orthologous dogfish enzyme. Direct calculations of thermodynamic activation parameters show that the cold-adapted fish enzymes are characterized by a lower activation enthalpy and a more negative entropy term. This appears to be a universal feature of psychrophilic enzymes, and it is found to originate from a higher flexibility of certain parts of the protein surface. We also carry out free energy simulations that address the differences in thermal stability and substrate binding affinity between the two cold-adapted enzymes, which only differ by a single mutation. These calculations capture the effects previously seen in in vitro studies and provide straightforward explanations of these experimental results. [ABSTRACT FROM AUTHOR]

Numerous fishes produce sounds and their transmission and detection may be hindered by increasing levels of anthropogenic noise. We investigated acoustic communication during dyadic contests between male croaking gouramis (Trichopsis vittata, Osphronemidae) in the presence and absence of white noise. We hypothesised that fish modify acoustic signalling in the presence of noise in order to maintain intraspecific communication. Under controlled laboratory settings we compared agonistic behaviour, visual and acoustic signalling between noise and no-noise conditions. Trichopsis vittata produced sounds that were significantly lower in level and higher in dominant frequency under noise treatments. No difference was found in visual signalling or temporal sound characteristics. This study indicates that noise does not affect the amount of signalling during agonistic behaviour in a highly vocal fish. No increase in sound level was observed in croaking gouramis, indicating that a Lombard effect is not present in all vocalising fish. The lack of a Lombard effect shows that sound communication is potentially hindered by (human-made) noise in fish, which may affect territory maintenance and reproduction. [ABSTRACT FROM AUTHOR]

Long‐read sequencing is driving a new reality for genome science in which highly contiguous assemblies can be produced efficiently with modest resources. Genome assemblies from long‐read sequences are particularly exciting for understanding the evolution of complex genomic regions that are often difficult to assemble. In this study, we utilized long‐read sequencing data to generate a high‐quality genome assembly for an Antarctic eelpout, Ophthalmolycus amberensis, the first for the globally distributed family Zoarcidae. We used this assembly to understand how O. amberensis has adapted to the harsh Southern Ocean and compared it to another group of Antarctic fishes: the notothenioids. We showed that selection has largely acted on different targets in eelpouts relative to notothenioids. However, we did find some overlap; in both groups, genes involved in membrane structure, thermal tolerance and vision have evidence of positive selection. We found evidence for historical shifts of transposable element activity in O. amberensis and other polar fishes, perhaps reflecting a response to environmental change. We were specifically interested in the evolution of two complex genomic loci known to underlie key adaptations to polar seas: haemoglobin and antifreeze proteins (AFPs). We observed unique evolution of the haemoglobin MN cluster in eelpouts and related fishes in the suborder Zoarcoidei relative to other Perciformes. For AFPs, we identified the first species in the suborder with no evidence of afpIII sequences (Cebidichthys violaceus) in the genomic region where they are found in all other Zoarcoidei, potentially reflecting a lineage‐specific loss of this cluster. Beyond polar fishes, our results highlight the power of long‐read sequencing to understand genome evolution. [ABSTRACT FROM AUTHOR]

An evolutionary development of the rheological characteristics of blood in the capillary blood flow is one of indicator of fishes' adaptation for the changing temperature conditions. Our earlier studies showed that large, nucleated erythrocytes of the Black Sea thornback ray (Raja clavata L.) and scorpionfish (Scorpaena porcus L.) had high ecto-ATPase activity. This activity varied from 3.0 to 3.9 and 6.0 to 10.0 nmol Fn/min/µL RBC in rays and scorpionfish, respectively. The use of thermal energy of ATP in the hydrolysis process made by ecto-ATPases in fish erythrocytes provided a heating of the plasma cells' membrane and the near-wall plasma layer with an aim to improve the rheological characteristics of blood in the capillary blood flow. To confirm the proposed assumption, we studied thermal phenomena in erythrocytes suspensions of fishes by continuous recording of temperature changes in the experimental cell with fishes' erythrocytes suspension with the addition of ATP (1 mg/mL) in vitro. A higher "thermal" activity of scorpionfish erythrocytes was established in comparison with erythrocytes of the thornback ray, which had the multiplicity of activity of ecto-ATPase in the plasma membranes of erythrocytes of the studied fishes. The presence of heat-producing activity of suspensions of erythrocytes of thornback ray and scorpionfish is evidence of the possible use of thermal energy of ATP hydrolysis by fish erythrocytes, both to maintain the functional state of the plasma membrane of red blood cells and to improve the rheological characteristics of blood in the capillary section of blood flow. [ABSTRACT FROM AUTHOR]

In species with alternative reproductive tactics, there is much empirical support that parasitically spawning males have larger testes and greater sperm numbers as an evolved response to a higher degree of sperm competition, but support for higher sperm performance (motility, longevity and speed) by such males is inconsistent. We used the sand goby (Pomatoschistus minutus) to test whether sperm performance differed between breeding‐coloured males (small testes, large mucus‐filled sperm‐duct glands; build nests lined with sperm‐containing mucus, provide care) and parasitic sneaker‐morph males (no breeding colouration, large testes, rudimentary sperm‐duct glands; no nest, no care). We compared motility (per cent motile sperm), velocity, longevity of sperm, gene expression of testes and sperm morphometrics between the two morphs. We also tested if sperm‐duct gland contents affected sperm performance. We found a clear difference in gene expression of testes between the male morphs with 109 transcripts differentially expressed between the morphs. Notably, several mucin genes were upregulated in breeding‐coloured males and two ATP‐related genes were upregulated in sneaker‐morph males. There was a partial evidence of higher sperm velocity in sneaker‐morph males, but no difference in sperm motility. Presence of sperm‐duct gland contents significantly increased sperm velocity, and nonsignificantly tended to increase sperm motility, but equally so for the two morphs. The sand goby has remarkably long‐lived sperm, with only small or no decline in motility and velocity over time (5 min vs. 22 h), but again, this was equally true for both morphs. Sperm length (head, flagella, total and flagella‐to‐head ratio) did not differ between morphs and did not correlate with sperm velocity for either morph. Thus, other than a clear difference in testes gene expression, we found only modest differences between the two male morphs, confirming previous findings that increased sperm performance as an adaptation to sperm competition is not a primary target of evolution. [ABSTRACT FROM AUTHOR]

The article "FISH: anatomical and adaptive curiosities" explores the shape and adaptations of aquatic organisms. It highlights that water density conditions the shape and speed of movement of organisms. The two main groups of fish are mentioned: chondrichthyans (cartilaginous) and osteichthyans (bony), and it is emphasized that tetrapods, including humans, belong to the osteichthyan group. It also discusses the adaptations of fish for hydrodynamics and the regulation of pressure in their swim bladder. The evolution of the way fish capture their food is discussed, and reflection is made on the impact of climate change on marine species and the environment in general. [Extracted from the article]

The mechanisms of biogeochemical adaptation of fish to survival in the historically contaminated Imandra Lake were studied. The role of trace elements in the protective functions of the organism and their importance in the readaptation of organisms to improving the habitat was established. An elevated S to Se ratio indicates a high antioxidant status of fish from the historically contaminated part of the lake, while an increased accumulation of Fe, Cu, and Se can serve as a marker of liver pathologies, and of Zn and Co, of kidney pathologies. [ABSTRACT FROM AUTHOR]

Sarcopterygian fishes are a taxon of bony fishes. They include lungfish and coelacanths (six species of lungfish and two species of coelacanths). Evolutionary adaptations arose with these fish, such as the appearance of lungs and paired lobed fins that help them move over the bottom of the sea. In the Devonian period, they came ashore, and tetrapods (amphibians, reptiles, and mammals) arose from them. Within immunology, they can teach us about the emergence of immunoglobulins D, A/X, and Y already present in amphibians. We have studied the genes of the immunoglobulins in the fish Sarcopterygii Neoceratodus forsteri and Protopterus annectens. In the first fish, we find that several loci for the constant chains of immunoglobulins are distributed across 4 chromosomes. We have found four genes for IgM, a gene for IgW and a gene for IgN. In the second, we find one locus with genes for IgN and IgM and another with one gene for IgW. With these sequences, together with those obtained in other publications, we have been able to study the possible evolution and emergence of immunoglobulin classes. We conclude that there are two evolutionary lineages, one focused on IgM and very conservative, and the other focused on IgW, which allows high variability. In the case of the animals that went to land, their IgD is formed only by domains whose origin is in the W lineage. IgA/X and IgY are unique since they arose from the recombination between the two evolutionary lineagess (M and W). In both IgA/X and IgY, the CH1 and CH2 domains come from domains whose origin is the W lineage, while their CH3 and CH4 derive from the M lineage. • Sarcopterygii have genes for three classes of immunoglobulins (IgM, IgW, and IgN). • The distribution of the loci is intermediate between that found in slamobranchs and terrestrial tetrapods. • There are two evolutionary lines of immunoglobulins. The IgM Line and the IgW Line. • The IgY and IgA/X of vertebrates that passed to land have a recombinational origin between the two lines. [ABSTRACT FROM AUTHOR]

Neotropical cichlids are a group of fish among which there are species with reversed sexual dichromatism, where females have carotenoid-based coloration that males lack. Carotenoid coloration can vary depending on the environment and the distribution of other types of chromatophores in the pigment pattern. The role of thyroid hormones (THs), one of the main signaling molecules regulating fish ontogeny, in the diversity of carotenoid coloration in Neotropical cichlid females remained poorly understood. In this work, using the species Amatitlania nigrofasciata, the effect of elevated TH level on the development of reversed sexual dichromatism was shown. Increases in TH signaling in experimental fish led to heterochrony in the development of the pigment pattern and phenotypic variability with the appearance of variants of carotenoid pigmentation similar to other Neotropical cichlid species. The extent of carotenoid-based ventral coloration of females depended on TH-induced changes in the melanistic pattern. The results obtained testify in favor of the important role of the TH signaling pathway in the diversification of the carotenoid coloration of Neotropical cichlids and provide new perspectives for studying the role of plasticity in the evolutionary adaptation of cichlid fishes. [ABSTRACT FROM AUTHOR]

Metallothioneins (MTs) are low-molecular weight sulfur-rich proteins, widely distributed in nature. They play a homeostatic role in the control and detoxification of metal ions. Previous studies indicated that MTs also have the capacity to scavenge reactive oxygen species. This study aimed to investigate the evolution of the protein in the notothenioid fish, evolved under the selective pressure of relatively high oxygen partial pressures, characteristics of cold Antarctic seawaters, and relatively high concentrations of metal ions, Cd and Cu in particular. The cDNA sequences of MT isoforms were characterized in members of the Nototheniidae, Bathydraconidae, Artedidraconidae, and Channichthyidae families. The phylogenetic relationships of MTs from these families and other teleosts were inferred by using Maximum Likelihood and Bayesian methods. The analysis of coding region and untranslated (UTR) sequences indicated the presence of two MT clades, each containing one of the two MT isoforms, MT-1 and MT-2. Our results indicated, for the first time for these proteins, that the evolution of MT genes has been characterized by strong purifying selection, whereas it did not observe any evidence of positive selection. In addition, phylogenetic analysis of the UTRs suggested that functional changes, in particular related to the MT-1 gene expression, had accompanied the duplication event. [ABSTRACT FROM AUTHOR]

Oysters are one of the main aquatic products produced in Taiwan. However, because of the gradual changes in the environment of the Waisanding Sandbar, the oyster farming environment along the coast of Chiayi is shrinking, leading to greater operational risk and uncertainty. This study adopted a three-stage method to investigate the socioeconomic uncertainty that fishing communities face regarding environmental changes and to understand the environmental risk and fishery management awareness of different stakeholders as well as their views on adaptation strategies. In-depth interviews were used in the first stage. In Stage 2, two-round focus group interviews were conducted to organize views on the environment and climate, the oyster industry and management, and adaptation strategies. In the final stage, the AHP method was adopted to analyze the opinions of different stakeholders. The results showed factors affecting environmental change, oyster industry, and management among different stakeholders as well as the cognitive differences within the corresponding adaptation strategies. Therefore, socioeconomic and ecology complexities and uncertainties should be considered for enhancing social capital and promoting risk communication, more diverse social–ecological system data to assist fishery governance, and oyster industry development and adaptation strategies. [ABSTRACT FROM AUTHOR]

Nutritional programming is a promising concept for promoting metabolic adaptation of fish to challenging conditions, such as the increase in water temperature. The present work evaluates in ovo arginine or glutamine supplementation as enhancers of zebrafish metabolic or absorptive capacity, respectively, at optimum (28 ºC) and challenging temperatures (32 ºC) in the long-term. Growth performance, free amino acids profile, methylation index and the activity levels of digestive and intermediary metabolism enzymes were analysed to assess the metabolic plasticity induced by an early nutritional intervention. Temperature affected fish larvae growth performance. At the end of the experimental period 28 ºC-fish showed higher dry weight than 32 ºC-fish. The effects of the early supplementation were reflected in the larval free amino acids profile at the end of the experiment. Higher methylation potential was observed in the ARG-fish. In ovo amino acid supplementation modulated the metabolic response in zebrafish larvae, however, the magnitude of this effect differed according to the amino acid and the temperature. Overall, arginine supplementation enhanced carbohydrates metabolism at 32 ºC. In conclusion, the present work suggests that in ovo arginine supplementation may promote a better adaptive response to higher temperatures. [ABSTRACT FROM AUTHOR]

Overcoming the negative effects of cold stress in Nile tilapia (Oreochromis niloticus) is of great interest for the overall aquaculture economy. Recent evidence suggests that microRNAs may regulate mechanisms of cold adaptation in fish and could be potential biomarkers of cold tolerance in these animals. However, information on how microRNAs regulating cold adaptation in fish are expressed in cold-tolerant and cold-sensitive fish is still scarce. Therefore, the aim of the present study is to investigate the relationship between a panel of previously identified differentially expressed microRNAs in fish exposed to low temperatures and their association with cold tolerance in Nile tilapia. To this end, fish were individualized based on their weight and length, and subjected to a critical thermal minimum (CTmin) test. Blood samples were collected before and after the CTmin test. After the CTmin, brain and liver tissues were collected. Fish were separated into cold-tolerant and cold-sensitive based on their CTmin results. Untreated fish were used as control. The relative expression of miR-9-3p, miR-135c, miR-9-5p, miR-30b, miR-122, miR-92a was assessed through qPCR. Additionally, qPCR was used to measure the mRNA relative expression of IGF-I and SCD in the tissues. Cortisol and biochemical parameters were determined in plasma samples. As a result, miR-92a was up-regulated in the liver of cold-sensitive fish and in the blood of cold-tolerant fish post-CTmin. miR-30b was up-regulated in the blood and liver of cold stressed fish. In the brain, miR-9-5p and miR-9-3p were up-regulated in cold-tolerant fish post-CTmin. Furthermore, miR-122 and miR-135c expression levels remained similar to the control post-CTmin. In addition, miR-122 and miR-92a were differentially expressed in the blood of cold-tolerant and cold-sensitive Nile tilapia pre-CTmin. Therefore, besides regulating fish cold acclimation responses differently in cold-tolerant and cold-sensitive fish, miRNAs may also regulate pre-existing physiological conditions that are determinant to cold tolerance in Nile tilapia. In the transcriptional level, SCD expression increased in both cold-tolerant and cold-sensitive fish post-CTmin. Cold-tolerant Nile tilapia post-CTmin had increased levels of plasma cholesterol and IGF-I mRNA in the liver, which could mean an adaptive advantage. The present findings provide new insights on the role of post-transcriptional regulation of cold tolerance in Nile tilapia. Furthermore, miRNAs differentially expressed in cold-tolerant Nile tilapia may be potential targets for the development of new biomarkers and aid in the breeding of cold-tolerant strains in this species. [Display omitted] • miR-92a and -30b are affected by acute cold stress in Nile tilapia blood and liver. • miR-9-3p and -5p are upregulated in cold tolerant Nile tilapia brain post-CTmin. • miR-122 and miR-92a are differentially expressed in cold tolerant tilapia pre-CTmin. • miR-122 and miR-92a are potential biomarkers of cold tolerance in Nile tilapia. • Plasma cholesterol and IGF-I mRNA in the liver may be linked to cold tolerance. [ABSTRACT FROM AUTHOR]

Long non-coding RNA (lncRNA) is a novel emerging type of competitive endogenous RNA (ceRNA) that performs key functions in multiple biological processes. However, little is known about the roles of lncRNA under hypoxia stress in fish. Here, vascular endothelial growth factor-Aa (vegfaa) was cloned in rainbow trout (Oncorhynchus mykiss), with the complete cDNA sequence of 2914 bp, encoding 218 amino acids. The molecular weight of the protein was approximately 25.33 kDa, and contained PDGF and VEGF_C domains. Time-course and spatial expression patterns revealed that LOC110520012 was a key regulator of rainbow trout in response to hypoxia stress, and LOC110520012, miR-206-y and vegfaa exhibited a ceRNA regulatory relationship in liver, gill, muscle and rainbow trout liver cells treated with acute hypoxia. Subsequently, the targeting relationship of LOC110520012 and vegfaa with miR-206-y was confirmed by dual-luciferase reporter analysis, and overexpression of LOC110520012 mediated the inhibition of miR-206-y expression in rainbow trout liver cells, while the opposite results were obtained after LOC110520012 silencing with siRNA. We also proved that vegfaa was a target of miR-206-y in vitro and in vivo , and the vegfaa expression and anti-proliferative effect on rainbow trout liver cells regulated by miR-206-y mimics could be reversed by LOC110520012. These results suggested that LOC110520012 can positively regulate vegfaa expression by sponging miR-206-y under hypoxia stress in rainbow trout, which facilitate in-depth understanding of the molecular mechanisms of fish adaptation and tolerance to hypoxia. • The full-length cDNA sequence of vegfaa was 2914 bp encoding 218 amino acids. • LOC110520012 and vegfaa were highly expressed under hypoxia stress. • vegfaa was shown to a direct target of miR-206-y in vitro and in vivo. • LOC110520012 acted as a ceRNA of vegfaa by sponging miR-206-y. • The inhibitory effect of miR-206-y on rainbow trout liver cell proliferation could be alleviated by LOC110520012. [ABSTRACT FROM AUTHOR]

Epigenetics plays a vital role in the interaction between living organisms and their environment by regulating biological functions and phenotypic plasticity. Considering that most aquaculture activities take place in open or natural habitats that are vulnerable to environmental changes. Promising findings from recent research conducted on various aquaculture species have provided preliminary evidence suggesting a link between epigenetic mechanisms and economically valuable characteristics. Environmental stressors, including climate changes (thermal stress, hypoxia, and water salinity), anthropogenic impacts such as (pesticides, crude oil pollution, nutritional impacts, and heavy metal) and abiotic factors (infectious diseases), can directly trigger epigenetic modifications in fish. While experiments have confirmed that many epigenetic alterations caused by environmental factors have plastic responses, some can be permanently integrated into the genome through genetic integration and promoting rapid transgenerational adaptation in fish. These environmental factors might cause irregular DNA methylation patterns in genes related to many biological events leading to organs dysfunction by inducing alterations in genes related to oxidative stress or apoptosis. Moreover, these environmental issues alter DNA/histone methylation leading to decreased reproductive competence. This review emphasizes the importance of understanding the effects of environmentally relevant issues on the epigenetic regulation of phenotypic variations in fish. The goal is to expand our knowledge of how epigenetics can either facilitate or hinder species' adaptation to these adverse conditions. Furthermore, this review outlines the areas that warrant further investigation in understanding epigenetic reactions to various environmental issues. [ABSTRACT FROM AUTHOR]

Simple Summary: Skull and jaw shape are critical to how an animal eats. The goal of this work was to examine how facial variation evolves and the genetic basis of these changes. We used two species of Lake Malawi cichlids with different facial shapes, one which has evolved to eat prey by suction feeding, a second that bites algae from rocks, as well as hybrid individuals generated by artificial mating of the two species. We found a series of changes in craniofacial structure including the shape of the lower jaw and throat region that impact how animals perform at suction feeding and biting. We then identified genetic regions that regulate these facial shapes. These genetic regions suggested that evolution of the senses, among other traits, may play an important role in facial evolution. Also, evolution of different parts of the face are controlled by distinct genetic regions. Despite this, cichlids that eat similar ways have similar facial shapes, suggesting that the function of jaw movement places certain limits on facial evolution in cichlid fishes. Overall, this work provides insights into how the face evolves, how these changes relate to feeding, and the genes and molecules that regulate craniofacial variation. Since Darwin, biologists have sought to understand the evolution and origins of phenotypic adaptations. The skull is particularly diverse due to intense natural selection on feeding biomechanics. We investigated the genetic and molecular origins of trophic adaptation using Lake Malawi cichlids, which have undergone an exemplary evolutionary radiation. We analyzed morphological differences in the lateral and ventral head shape among an insectivore that eats by suction feeding, an obligate biting herbivore, and their F2 hybrids. We identified variation in a series of morphological traits—including mandible width, mandible length, and buccal length—that directly affect feeding kinematics and function. Using quantitative trait loci (QTL) mapping, we found that many genes of small effects influence these craniofacial adaptations. Intervals for some traits were enriched in genes related to potassium transport and sensory systems, the latter suggesting co-evolution of feeding structures and sensory adaptations for foraging. Despite these indications of co-evolution of structures, morphological traits did not show covariation. Furthermore, phenotypes largely mapped to distinct genetic intervals, suggesting that a common genetic basis does not generate coordinated changes in shape. Together, these suggest that craniofacial traits are mostly inherited as separate modules, which confers a high potential for the evolution of morphological diversity. Though these traits are not restricted by genetic pleiotropy, functional demands of feeding and sensory structures likely introduce constraints on variation. In all, we provide insights into the quantitative genetic basis of trophic adaptation, identify mechanisms that influence the direction of morphological evolution, and provide molecular inroads to craniofacial variation. [ABSTRACT FROM AUTHOR]

Harsh environments provide opportunities to study how different species adapt, at the molecular level, to similar environmental stressors. High hydrostatic pressure, low temperature, and absence of sunlight in the deep-sea environment are challenging conditions for gene expression, cell morphology and vision. Adaptation of fish to this environment appears independently in at least 22 orders of fish, but it remains uncertain whether these adaptations represent convergent evolution. In this study, we performed comparative genomic analysis of 80 fish species to determine genetic evidences for adaptations to the deep-sea environment. The 80 fishes were divided into six groups according to their order. Positive selection and convergent evolutionary analysis were performed and functional enrichment analysis of candidate genes was performed. Positively selected genes (pik3ca , pik3cg , vcl and sphk2) were identified to be associated with the cytoskeletal response to mechanical forces and gene expression. Consistent signs of molecular convergence genes (grk1 , ednrb , and nox1) in dark vision, skin color, and bone rarefaction were revealed. Functional assays of Grk1 showed that the convergent sites improved dark vision in deep-sea fish. By identifying candidate genes and functional profiles potentially involved in cold, dark, and high-pressure responses, the results of this study further enrich the understanding of fish adaptations to deep-sea environments. [ABSTRACT FROM AUTHOR]

Ecological transitions across salinity boundaries have led to some of the most important diversification events in the animal kingdom, especially among fishes. Adaptations accompanying such transitions include changes in morphology, diet, whole-organism performance, and osmoregulatory function, which may be particularly prominent since divergent salinity regimes make opposing demands on systems that maintain ion and water balance. Research in the last decade has focused on the genetic targets underlying such adaptations, most notably by comparing populations of species that are distributed across salinity boundaries. Here, we synthesize research on the targets of natural selection using whole-genome approaches, with a particular emphasis on the osmoregulatory system. Given the complex, integrated and polygenic nature of this system, we expected that signatures of natural selection would span numerous genes across functional levels of osmoregulation, especially salinity sensing, hormonal control, and cellular ion exchange mechanisms. We find support for this prediction: genes coding for V-type, Ca2+, and Na+/K+-ATPases, which are key cellular ion exchange enzymes, are especially common targets of selection in species from six orders of fishes. This indicates that while polygenic selection contributes to adaptation across salinity boundaries, changes in ATPase enzymes may be of particular importance in supporting such transitions. [ABSTRACT FROM AUTHOR]

Periophthalmodon septemradiatus (Hamilton, 1822) is a unique mudskipper living in the mudbanks from estuarine to riverine regions in the Vietnamese Mekong Delta (VMD), but there is no data on its growth patterns and condition factors that are helpful for fish resource assessment and adaptation understanding. This study was conducted at five sites, from the lower (Soc Trang province) to middle (Can Tho city) and upper (An Giang province) reaches of Bassac River in VMD, to provide knowledge on growth patterns and condition factors to this mudskippers. Fish samples were caught using traps and hands for 24 months, from July 2017 to June 2019, at these five sites. The total length and weight of 3,417 individuals (1,340 females and 2,077 males) varied by sex, season and site (p < 0.001 for all cases). This species exhibited a positive allometric type as the slope (b = 3.06 ± 0.01) of the length-weight relationship (LWR) was >3 (p < 0.001) for both sexes. The growth pattern changed with sex as mudskipper showed isometry in females but positive allometry in males. Maturity also affected fish growth type since it shifted from negative allometry in immature groups to positive allometry in mature groups. The growth pattern of fish changed from isometry in the dry season to positive allometry in the wet season. The mudskipper showed isometry at the lower reaches in Soc Trang but positive allometry at the middle and upper reaches in Can Tho and An Giang. The condition factor (CF) did not change according to sex, size and season, but with month and site variables. The present environmental condition in these studied sites tended to be not good enough for this fish as CF (0.95 ± 0.01) was less than 1 (p < 0.001). The findings provided basic information on the growth and adaptation of P. septemradiatus being helpful in fish adaptation understanding and resource conservation in VMD. [ABSTRACT FROM AUTHOR]

Background: Scatophagus argus, an estuarine inhabitant, can rapidly adapt to different salinity environments. However, the knowledge of the molecular mechanisms underlying its strong salinity tolerance remains unclear. The gill, as the main osmoregulatory organ, plays a vital role in the salinity adaptation of the fish, and thus relative studies are constructive to reveal unique osmoregulatory mechanisms in S. argus. Results: In the present study, iTRAQ coupled with nanoLC-MS/MS techniques were employed to explore branchial osmoregulatory mechanisms in S. argus acclimated to different salinities. Among 1,604 identified proteins, 796 differentially expressed proteins (DEPs) were detected. To further assess osmoregulatory strategies in the gills under different salinities, DEPs related to osmoregulatory (22), non-directional (18), hypo- (52), and hypersaline (40) stress responses were selected. Functional annotation analysis of these selected DEPs indicated that the cellular ion regulation (e.g. Na+-K+-ATPase [NKA] and Na+-K+-2Cl− cotransporter 1 [NKCC1]) and ATP synthesis were deeply involved in the osmoregulatory process. As an osmoregulatory protein, NKCC1 expression was inhibited under hyposaline stress but showed the opposite trend in hypersaline conditions. The expression levels of NKA α1 and β1 were only increased under hypersaline challenge. However, hyposaline treatments could enhance branchial NKA activity, which was inhibited under hypersaline environments, and correspondingly, reduced ATP content was observed in gill tissues exposed to hyposaline conditions, while its contents were increased in hypersaline groups. In vitro experiments indicated that Na+, K+, and Cl− ions were pumped out of branchial cells under hypoosmotic stress, whereas they were absorbed into cells under hyperosmotic conditions. Based on our results, we speculated that NKCC1-mediated Na+ influx was inhibited, and proper Na+ efflux was maintained by improving NKA activity under hyposaline stress, promoting the rapid adaptation of branchial cells to the hyposaline condition. Meanwhile, branchial cells prevented excessive loss of ions by increasing NKA internalization and reducing ATP synthesis. In contrast, excess ions in cells exposed to the hyperosmotic medium were excreted with sufficient energy supply, and reduced NKA activity and enhanced NKCC1-mediated Na+ influx were considered a compensatory regulation. Conclusions: S. argus exhibited divergent osmoregulatory strategies in the gills when encountering hypoosmotic and hyperosmotic stresses, facilitating effective adaptabilities to a wide range of environmental salinity fluctuation. [ABSTRACT FROM AUTHOR]

This study aimed to understand cold stress adaptations mechanism in fish. Thus, the transcriptional response to cold conditions in Gymnocypris eckloni was evaluated using RNA-seq and microRNA (miRNA)-seq analyses. Low-temperature (LT) group G. eckloni was cultivated outdoors in waters cooled to 2-4°C for 3 weeks, while individuals in the control temperature (CT) group were exposed to 14-16°C. Significantly different responses were observed in both mRNA and miRNA expression profiles, with more mRNAs (1,833 and 1,869 mRNAs were up- and downregulated, respectively) and fewer miRNAs (15 and 6 were up- and downregulated, respectively) observed in the LT group individuals relative to the CT group individuals. A miRNA-mRNA network involved in the regulation of G. eckloni responses to cold stress was constructed; this network included ubiquitin-mediated proteolysis, protein processing, and oxidative phosphorylation. These results provided new insights into mechanisms of cold tolerance by fish, including decreased metabolic activity in addition to proteolysis. [ABSTRACT FROM AUTHOR]

The study was focused on determining transcription levels of γM-crystallin genes in the eye lens of a common carp Cyprinus carpio. The transcription was detected by quantitative RT-PCR, and its relative level was quantified in 5 genes of γM-crystallins and crystallin-like proteins in C. carpio aged 4, 10 and 14 months. In all age groups, the specificity of GCM1, GCM1L, GCM2L, GCM2L3 gene expression in the lenses was found. GCM2 gene expression, apart from the lenses, was also detected in the muscles, liver and brain. Analysis of the role of the amino acid sequence of the identified γM-crystallins in the formation of the refractive properties of the lens was performed based on the assessment of calculated refractive index increments. It is assumed that high values of the refractive index of the lens in C. carpio are due not so much to a relative content of amino acids in γM-crystallins as to their sequences, which ensure the tertiary packing density of these proteins, as well as by γM-crystallin concentrations. To identify conserved domains and evolutionary relationships between γM-crystallins in fish of different taxa, a multiple alignment of amino acid sequences was performed, and a phylogenetic tree was constructed using the neighbor-joining clustering method. The high level of homology, the presence of 26 conserved regions, and the phylogenetic proximity of the compared lens crystallins in the clade Teleostomi may indicate an evolutionary consolidation of the spatial structure of these proteins and their important role in the adaptation of the fish eye's optical apparatus to vision in water. [ABSTRACT FROM AUTHOR]

Royal Decree 502/2022 regulates fishing in Spain's national fishing grounds, with the aim of improving the adaptation of fishing vessels to fishery resources and ensuring economic, social, and environmental sustainability. Common rules for management and governance are established for different fishing modalities, as well as specific measures to ensure sustainability and reduce impacts on marine ecosystems. The decree also includes provisions on fishing effort, changes in fishing modality, exchanges and changes in census, technical characteristics of fishing gear, and measures to mitigate accidental catches of protected species. The decree will come into effect on June 29, 2022, and repeals previous regulations related to fishing in national fishing grounds. [Extracted from the article]

This study aims to mine a previously developed continuous-flow competitive exclusion culture (CFCEC) originating from the Tilapia gut microbiome as a rational and efficient autochthonous probiotic strain recovery source. Three isolated strains were tested on their adaptability to host gastrointestinal conditions, their antibacterial activities against aquaculture bacterial pathogens, and their antibiotic susceptibility patterns. Their genomes were fully sequenced, assembled, annotated, and relevant functions inferred, such as those related to pinpointed probiotic activities and phylogenomic comparative analyses to the closer reported strains/species relatives. The strains are possible candidates of novel genus/species taxa inside Lactococcus spp. and Priestia spp. (previously known as Bacillus spp.) These results were consistent with reports on strains inside these phyla exhibiting probiotic features, and the strains we found are expanding their known diversity. Furthermore, their pangenomes showed that these bacteria have indeed a set of so far uncharacterized genes that may play a role in the antagonism to competing strains or specific symbiotic adaptations to the fish host. In conclusion, CFCEC proved to effectively allow the enrichment and further pure culture isolation of strains with probiotic potential. [ABSTRACT FROM AUTHOR]

Differences in genomic architecture between populations, such as chromosomal inversions, may play an important role in facilitating adaptation despite opportunities for gene flow. One system where chromosomal inversions may be important for eco‐evolutionary dynamics is in freshwater fishes, which often live in heterogenous environments characterized by varying levels of connectivity and varying opportunities for gene flow. In the present study, reduced representation sequencing was used to study possible adaptation in n = 345 walleye (Sander vitreus) from three North American waterbodies: Cedar Bluff Reservoir (Kansas, USA), Lake Manitoba (Manitoba, Canada), and Lake Winnipeg (Manitoba, Canada). Haplotype and outlier‐based tests revealed a putative chromosomal inversion that contained three expressed genes and was nearly fixed in walleye assigned to Lake Winnipeg. These patterns exist despite the potential for high gene flow between these proximate Canadian lakes, suggesting that the inversion may be important for facilitating adaptive divergence between the two lakes despite gene flow. However, a specific adaptive role for the putative inversion could not be tested with the present data. Our study illuminates the importance of genomic architecture consistent with local adaptation in freshwater fishes. Furthermore, our results provide additional evidence that inversions may facilitate local adaptation in many organisms that inhabit connected but heterogenous environments. [ABSTRACT FROM AUTHOR]

Nitric Oxide (NO) is a free radical with numerous critical signaling roles in vertebrate physiology. Similar to mammals, in the teleost system the generation of sufficient amounts of NO is critical for the physiological function of the cardiovascular system. At the same time, NO amounts are strictly controlled and kept within basal levels to protect cells from NO toxicity. Changes in oxygen tension highly influence NO bioavailability and can modulate the mechanisms involved in maintaining the NO balance. While NO production and signaling appears to have general similarities with mammalian systems, the wide range of environmental adaptations made by fish, particularly with regards to differing oxygen availabilities in aquatic habitats, creates a foundation for a variety of in vivo models characterized by different implications of NO production and signaling. In this review, we present the biology of NO in the teleost cardiovascular system and summarize the mechanisms of NO production and signaling with a special emphasis on the role of globin proteins in NO metabolism. [ABSTRACT FROM AUTHOR]

Fish are the main source of long-chain polyunsaturated fatty acids (LC-PUFA) for human consumption. In the process of evolution via natural selection, adaptation to distinct environments has likely driven changes in the endogenous capacity for LC-PUFA biosynthesis between marine and freshwater fishes. However, the molecular mechanisms underlying adaptive changes in this metabolic pathway are poorly understood. Here, we compared the transcriptional regulation of elongation of very long chain fatty acids protein 5 (Elovl5), which is one of the critical enzymes in LC-PUFA biosynthesis pathway, in marine large yellow croaker (Larimichthys crocea) and freshwater rainbow trout (Oncorhynchus mykiss). Comparative transcriptomic and absolute mRNA quantification analyses revealed that the expression of elovl5 in rainbow trout was markedly higher than that in large yellow croaker. Correspondingly, the number of chromatin accessible areas in the regulatory region of elovl5 in rainbow trout was higher than in large yellow croaker, which revealed that chromatin accessibility in the regulatory region of elovl5 in rainbow trout was higher. Furthermore, the differences in sequence and activity of the elovl5 promoter were observed between rainbow trout and large yellow croaker, and transcription factors including CCAAT/enhancer-binding protein β (CEBPβ), GATA binding protein 3 (GATA3) and upstream stimulatory factor 2 (USF2) displayed different regulatory roles on elovl5 expression between the two species. We propose that changes in the gene regulatory region driven by natural selection likely play a key role in differences in elovl5 expression and the activity of Elovl5, which may influence the LC-PUFA biosynthesis capacities of rainbow trout and large yellow croaker. These findings may also provide opportunities to improve the quality of aquatic products and, consequently, human health. [ABSTRACT FROM AUTHOR]

Sinocyclocheilus represents a rare, freshwater teleost genus endemic to China that comprises the river-dwelling surface fish and the cave-dwelling cavefish. Using a combinatorial approach of quantitative lipidomics and mass-spectrometry imaging (MSI), we demonstrated that neural compartmentalization of lipid distribution and lipid metabolism is associated with the evolution of troglomorphic traits in Sinocyclocheilus. Attenuated docosahexaenoic acid (DHA) biosynthesis via the Δ4 desaturase pathway led to reductions in DHA-phospholipids in cavefish cerebellum. Instead, cavefish accumulates arachidonic acid-phospholipids that may disfavor retinotectal arbor growth. Importantly, MSI of sulfatides coupled with immunostaining of myelin basic protein and transmission electron microscopy images of hindbrain axons revealed demyelination in cavefish raphe serotonergic neurons. Demyelination in cavefish parallels the loss of neuroplasticity governing social behavior such as aggressive dominance. Outside the brain, quantitative lipidomics and qRT-PCR revealed systemic reductions in membrane esterified DHAs in the liver, attributed to suppression of genes along the Sprecher pathway (elovl2 , elovl5 , and acox1). Development of fatty livers was observed in cavefish; likely mediated by an impeded mobilization of storage lipids, as evident in the diminished expressions of pnpla2 , lipea , lipeb , dagla , and mgll ; and suppressed β-oxidation of fatty acyls via both mitochondria and peroxisomes as reflected in the reduced expressions of cpt1ab , hadhaa , cpt2 , decr1, and acox1. These neurological and systemic metabolic adaptations serve to reduce energy expenditure, forming the basis of recessive evolution that eliminates nonessential morphological and behavioral traits and giving cavefish a selective advantage to thrive in caves where proper resource allocation becomes a major determinant of survival. [ABSTRACT FROM AUTHOR]

Hypoxia, largely triggered by global warming and water contamination, has become an environmental issue of great concern, posing a great threat to aquatic ecosystem. As one of the world's most economically important fish, rainbow trout (Oncorhynchus mykiss) is extremely intolerant of hypoxic environments, however, little is known about the roles of non-coding RNAs (ncRNAs) in the response of rainbow trout to hypoxia stress. Herein, effects of moderate (Tm12L) and severe hypoxia for 12 h (Ts12L) and 12 h reoxygenation on histology, biochemical parameters (antioxidant, metabolism and immunity) and transcriptome (lncRNA, miRNA and mRNA) in rainbow trout liver were investigated. We further validated the regulatory relationships between LOC110519952, novel-m0023-5p and glut1a via dual‑luciferase reporter, overexpression and silencing assays. Compared with Tm12L, the liver in Ts12L showed more severe oxidative damage. Anaerobic, lipid and protein metabolism was enhanced under hypoxia stress, especially in Ts12L. We also found that Tm12L could strengthen innate immune response, which was inhibited in Ts12L. Besides, several hypoxia-related genes (glut1a , vegfaa , hmox , epoa , foxo1a and igfbp1) and ceRNA networks were identified from 1824, 427 and 545 differentially expressed mRNAs, miRNAs and lncRNAs, including LOC118965299-novel-m0179-3p- epoa , LOC110519952-novel-m0023-5p- glut1a , MSTRG.7382.2-miR-184-y- hmox and LOC110520012-miR-206-y- vegfaa. Through in vitro and in vivo functional analysis, we demonstrated that glut1a is a target of novel-m0023-5p, and LOC110519952 can positively regulate glut1a by targeting novel-m0023-5p. Introduction of LOC110519952 could attenuate the promoting effects of novel-m0023-5p on rainbow trout liver cell viability and proliferation. This study highlights the differences in the regulatory mechanism of rainbow trout under different concentrations of hypoxia stress and provides valuable data for further research on the molecular mechanisms of fish adaptation to hypoxic environments. [Display omitted] • Anaerobic metabolism was strongly enhanced under severe hypoxia. • Innate immune response was inhibited under severe hypoxia. • Numerous hypoxia-related genes and lncRNA-miRNA-mRNA networks were identified. • LOC110519952 functioned as ceRNA to target glut1a by sponging novel-m0023-5p. • Overexpressed novel-m0023-5p promoted cell viability and proliferation. [ABSTRACT FROM AUTHOR]