Search Results (69)

Emerging contaminants constitute a growing pressure on river ecosystems due to their persistence, chemical diversity, and ecotoxicological effects. The objective of this study was to analyze the presence of these compounds in muscle tissue across a range of aquatic species, including benthic fish (Gobio lozanoi, Cobitis sp.), nektonic species (Salmo trutta, Lepomis gibbosus), diadromous species (Anguilla anguilla, Petromyzon marinus, in the larval stage), generalist species (Pseudochondrostoma duriense), and crustaceans (Procambarus clarkii). Concentrations were determined using LC-MS/MS, grouping the compounds into different chemical families (e.g., pharmaceuticals, personal care products, industrial compounds, and other emerging contaminants). The results showed significant differences both among species and among compound families. At the interspecific level, Petromyzon marinus (larvae) exhibited the highest total concentrations, followed by Salmo trutta and benthic species such as Gobio lozanoi and Cobitis sp. Intermediate values were observed in Pseudochondrostoma duriense and Lepomis gibbosus, while Anguilla anguilla showed moderate levels. Procambarus clarkii displayed notable accumulation, especially of sediment-associated compounds. Analysis by compound families revealed distinct patterns: pharmaceutical and personal care compounds showed a relatively homogeneous distribution among species, whereas more hydrophobic and industrial compounds tended to accumulate in species with higher lipid content or greater benthic exposure. In particular, benthic species (lamprey larvae, gudgeon, spined loach, and crayfish) showed higher accumulation of sediment-associated compounds, confirming their role as contaminant reservoirs. Lamprey larvae, which exhibit filter-feeding behavior and remain buried in fine sediments for several years, showed high accumulation of multiple contaminant families, highlighting the importance of this life stage as an indicator of environmental contamination. The results demonstrate the coexistence of different accumulation mechanisms: (i) direct exposure to sediment, (ii) trophic biomagnification, and (iii) accumulation linked to the physicochemical properties of the compounds. This combined approach by species and contaminant families allows for a more comprehensive assessment of the ecological status of the system. Finally, the relevance of including multiple taxonomic groups and life cycle stages in monitoring programs is emphasized, especially in vulnerable species such as Petromyzon marinus. Full article

Background: The Taiwanese loach (Paramisgurnus dabryanus ssp. Taiwan, Dabry de Thiersant, 1872.) is an economically important aquaculture species in East Asia, and its body color directly affects its ornamental and market value. Our research group recently discovered a golden-red mutant, named “Gan Hong No. 1” (MR), within a wild-type (WT) population. During embryogenesis, MR individuals exhibit almost no melanophore deposition, and after hatching, xanthophores and erythrophores appear sequentially, suggesting that the body color variation likely originates from alterations in the gene regulatory network during early development. Objective: To systematically compare the transcriptomes of WT and MR-Taiwanese loach during early development, to identify the key regulatory pathways underlying red body color formation from a temporal perspective, to test whether the classical melanin synthesis pathway is impaired, and to provide a theoretical basis for selective breeding of body color traits. Methods: High-throughput transcriptome sequencing was performed on eight early developmental stages (0, 5, 10, 15, 20, 23, 28 and 43 h post-fertilization) of both loach types. Differential expression analysis, time-series trend analysis, and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment were used to systematically characterize gene expression dynamics. Transcriptomic data validation was performed using real-time PCR. Results: In MR, the core transcription factor mitfa was significantly downregulated, whereas the expression of melanin synthesis genes such as kita and dct showed no significant difference, indicating that the impairment of melanogenesis is caused by mitfa downregulation. Trend analysis and pathway enrichment revealed that in MR embryos, pathways related to oxidative stress, unsaturated fatty acid biosynthesis, C-type lectin receptor signaling, p53 signaling, and apoptosis were significantly activated, while the thyroid hormone synthesis pathway was markedly upregulated. In WT, these pathways showed the opposite trend. qRT-PCR results were consistent with the transcriptome data. Conclusions: This study demonstrates that downregulation of mitfa serves as the initial trigger for red body color variation in the Taiwanese loach. This mutation impedes melanin synthesis and concurrently activates a coordinated regulatory network involving oxidative stress, immune inflammation, and thyroid hormone signaling. Accumulation of unsaturated fatty acids alleviates oxidative damage and supports carotenoid deposition, while immune signals eliminate aberrant melanocytes and promote compensatory generation of red and yellow chromatophores. The upregulated thyroid hormone further fine-tunes pigment cell differentiation. For the first time in a cobitid species, this study elucidates the mitfa-mediated, multi-pathway synergistic molecular mechanism driving the transition from melanin-based to carotenoid/pteridine-based red coloration in fish, thereby providing a theoretical reference for molecular breeding of body color in aquaculture. Full article

Neolissochilus heterostomus, a cyprinid fish endemic to Yunnan Province, China, is highly valued for both ornamental and edible purposes, yet its wild populations are currently declining and classified as endangered. In this study, we present a chromosome-level genome assembly of N. heterostomus, utilizing the PacBio HiFi and Hi-C strategies. The assembled genome spans 1793.99 Mb and is anchored to 50 chromosomes, comprising a total of 50,203 genes. Genomic features and chromosomal karyotype data recorded in the present study are consistent with an allotetraploid origin for N. heterostomus. Comparative genomics shows that N. heterostomus shares a close phylogenetic relationship with another allotetraploid fish, the common carp Cyprinus carpio. In total, 4687 expanded and 1365 contracted gene families were identified in N. heterostomus. Further enrichment analyses indicated an overrepresentation of metabolism-related pathways among the expanded and positively selected gene families, whereas the contracted gene families were enriched in reproduction- and embryonic development-related pathways. Reproductive observations further indicate that N. heterostomus produces fewer eggs than other cyprinid species characterized by relatively long embryonic development periods (106.1 h; accumulated temperature: 2260.6 °C·h), including common carp, goldfish (Carassius auratus), grass carp (Ctenopharyngodon idella), pond loach (Misgurnus anguillicaudatus), and blunt snout bream (Megalobrama amblycephala). These findings suggest a potential association between metabolism-related genomic features and reproductive traits, although functional validation remains necessary. Overall, this study may offer insights into the polyploidization, metabolic, and reproductive traits of N. heterostomus, thereby providing genomic and biological resources that may support future studies relevant to the conservation and management of this endangered species. Full article

Invasive fish species pose a major threat to freshwater ecosystems by outcompeting native species and altering habitat conditions, leading to biodiversity loss. The Plitvice Lakes National Park, a UNESCO World Heritage site in Croatia, harbors a unique but species-poor native fish community, including Danube trout (Salmo labrax), Italian minnow (Phoxinus lumaireul), Italian golden loach (Sabanejewia larvata), and Italian spined loach (Cobitis bilineata). However, human-introduced species such as rainbow trout (Oncorhynchus mykiss), rudd (Scardinius erythrophthalmus), chub (Squalius cephalus), and northern pike (Esox lucius) have established thriving populations, with rudd emerging as the dominant invasive species. To mitigate their ecological impact, targeted removal efforts were implemented using casting nets and electrofishing, aiming to reduce invasive populations while minimizing harm to native species. Monitoring activities, performed during the course of the removal project, revealed significant declines in invasive fish abundance, demonstrating the effectiveness of these management interventions. Rudd abundance in Prošćansko Lake decreased by 56.9% and biomass by 69.7% over three years, while rainbow trout abundance in the B-C-M system declined by 92.7%, and its distribution shrank to a single locality, indicating strong population reduction. These findings highlight the importance of implementing active conservation measures to control invasive fish populations, thereby improving the status of native fish communities and preserving ecological balance. Full article

Loach (Misgurnus anguillicaudatus) is a small benthic fish favored by consumers in East Asia. Female loaches exhibit greater production value due to their larger size and higher meat yield. Therefore, controlling the sex of loach should be studied to implement an all-female breeding strategy. This study identified sex-related SNP markers and candidate genes in loach through GWAS. Genotyping male and female populations with WGRS revealed 84 SNPs labeled as associated with sex. Distinct SNP peaks appeared on Chr6 and Chr3, with over half of the sex-associated SNPs located on Chr6. Within these sex-associated regions, 15 key candidate genes related to sex and reproduction were identified, including hemgn and foxl2a. Among these genes, pik3cb on Chr3 and hhip, cntln, and pard3ba on Chr6 have multiple sex-associated haplotypes that can be utilized for subsequent monosex breeding. Notably, a highly male-linked SNP marker was identified on pard3ba, whose genotype is consistent with the male heterogamete (XX/XY). Through gene enrichment analysis and expression validation, signaling pathways such as TGF-β, FoxO, and mTOR were identified as being involved in sex regulation. This study provides molecular markers for sex-controlled breeding in loach, facilitating in-depth research into the mechanisms of sex regulation in loach. Full article

Mud loach (Misgurnus mizolepis) is a freshwater fish widely farmed in inland aquaculture owing to its nutritional value. However, failure to distinguish Chinese from Korean mud loach negatively affects the distribution economy and food safety regulation. Untargeted profiling was previously used to determine the origin of mud loaches, and N-acetylhistidine and anserine were selected as biomarker candidates. However, their quantitative verification and practical applicability for origin discrimination have not been thoroughly investigated. In this study, mud loaches of different geographical origins were analyzed using liquid chromatography-ultraviolet and liquid chromatography-tandem mass spectrometry to quantify the two metabolites, followed by statistical and receiver operating characteristic (ROC) analyses to evaluate their discriminative performance. Compared with Korean mud loaches, Chinese mud loaches showed significantly higher concentrations of both metabolites. The area under the curve values for N-acetylhistidine and anserine were 0.88 and 0.89, respectively, reflecting high sensitivity and specificity for discriminating between Korean and Chinese mud loaches. Cutoff values were established for reliably distinguishing the geographical origin of mud loaches. The established approach based on N-acetylhistidine and anserine can be used to determine the geographical origin of mud loach. Full article

Within the freshwater fish order Cypriniformes, loaches form a monophyletic lineage comprising nine families with more than 1400 species. Secondary sexual dimorphism is widespread among loach families, most notably in the form of enlarged pectoral fins and tubercles or other hard structures on the pectoral fin in adult males. To date, the family Botiidae, phylogenetically sister to all other loach families, was reported to lack such sexually dimorphic structures, leading to the hypothesis that the common ancestor of loaches did not exhibit sexual dimorphism. Here, we report the presence of sexual dimorphism in eight species of Botiidae: Leptobotia bellacauda, L. guilinensis, L. microphthalma, L. taeniops, L. tchangi, Parabotia fasciatus, Sinibotia pulchra, and S. robusta. In all species, adult males possess longer pectoral fins than females. Additionally, males of L. guilinensis and L. tchangi exhibit larger pelvic fins, while males of L. microphthalma have larger anal fins. In L. bellacauda, L. microphthalma, and L. tchangi, portions of the dorsal surface of the pectoral fin bear rows of tubercles. The three genera displaying sexual dimorphism belong to two different subfamilies, demonstrating that sexual dimorphism is widespread across Botiidae and not restricted to a single genus or subfamily. Our results show that sexual dimorphism is present in the most basal family of loaches, suggesting that it represents a synapomorphy of loach fishes. Full article

Hulun Lake, a UNESCO Biosphere Reserve, faces mounting threats from extreme climate events and anthropogenic pressures, highlighting the need for robust biodiversity monitoring. Environmental DNA (eDNA) has emerged as a promising tool for aquatic biomonitoring, yet different bioinformatic pipelines—such as Amplicon Sequence Variant (ASV) and Operational Taxonomic Unit (OTU) clustering—may yield divergent results. This study compares ASV and OTU clustering approaches in eDNA metabarcoding alongside traditional capture-based surveys to assess fish diversity in Hulun Lake. Across all methods, we identified 43 taxa (40 species), including the critically endangered Acheilognathus hypselonotus and vulnerable Choi’s spiny loach (Cobitis choii). While eDNA methods detected 2~3 times more species than in nets (13 species), strong methodological correlations (p < 0.001) were observed between net frequencies and eDNA-derived relative abundances (based on both ASV and OTU datasets using 4th-root and log transformations). Clustering analysis of capture-based data revealed four distinct ecological zones: the areas near tourist facilities, Wuerxun River inflow region, Wulan Nuoer Lake (connected via the Wuerxun River), and the Lake Centre. Significant spatial variation (p < 0.05) between these four zones was found in eDNA datasets, whereas nets captured more heterogeneous patterns, consistent with previous studies. Community structures were shaped by both generalists (e.g., Cyprinus carpio, Hemiculter bleekeri) and habitat specialists such as Amur catfish (Silurus asotus). The Lake Centre hosted a unique assemblage, likely due to reduced human disturbance. Overall, both eDNA clustering methods outperformed capture-based survey in detecting species richness and offered semi-quantitative insights. However, discrepancies between ASV and OTU approaches were evident in resolving fine-scale community differences. We recommend an integrated monitoring strategy that combines the sensitivity of eDNA with the abundance resolution of net captured to inform spatially targeted conservation and habitat protection in this vulnerable ecosystem. Full article

Hybridization and polyploidization are key evolutionary forces shaping fish biodiversity. But their interaction with environmental factors, such as temperature, remains poorly understood. This study examined how maternal genome composition and incubation water temperature influence the hatching success, ploidy structure, morphology and early growth of polyploid Cobitis larvae. Crosses were performed using triploid Cobitis females with three genomic compositions (EEN, EET and ETN), representing combinations of genomes from C. elongatoides (E), C. taenia (T) and C. tanaitica (N), and diploid C. taenia males as sperm donors. Fertilized eggs were incubated at 18 °C, 22 °C and 28 °C. Triploid and tetraploid offspring occurred in comparable proportions on average across all groups, but developmental abnormalities were significantly more observed in tetraploid larvae. Females with EET and ETN genomes achieved higher hatching success than those with the EEN genome. Temperature had a pronounced effect on developmental timing and success: hatching occurred earliest at 28 °C, but survival decreased and abnormalities were most frequent. These results highlight genome- and temperature-dependent trade-offs in early development of Cobitis hybrids, providing new insight into reproductive dynamics and the potential resilience of polyploid systems under climate warming. Full article

Wetland diversity and associated wildlife is declining globally. The Szaporca Old-Drava oxbow, one of Hungary’s first wetlands designated under the Ramsar Convention, has been threatened by desiccation, prompting the implementation of water replenishment interventions. This study aimed to determine which aquatic vertebrate species can be detected using bottle traps in the oxbow and whether the traps’ efficiency and capture success change following hydrological restoration. Our results showed that the relative frequency of smooth newts caught with bottle traps was 10%, while that of other amphibians (Danube crested newt, common spadefoot toad, edible frog) and fish (European weather loach, European mudminnow, Danube whitefin gudgeon) species did not even reach 1%. Based solely on the relative frequency data of the smooth newt, we found that both the capture efficiency (10.4% vs. 3%) and capture success (17% vs. 7.4%) of bottle traps significantly declined following an increase in water volume in the oxbow. Sex ratio patterns also shifted markedly: in the year of water scarcity, the male-to-female ratio of smooth newt was 2.7:1, whereas during water-abundant conditions it increased to 7:1. Water replenishment raised the water level by nearly one meter, resulting in the partial inundation of terrestrial vegetation and consequent habitat alterations. While water supplementation clearly supports the persistence of rare, protected, strictly protected and endemic aquatic species, our findings highlight the importance of considering hydrological conditions when interpreting the results of long-term monitoring in wetland ecosystems. Full article

The diversity and distribution of fish in the water bodies of the Black Irtysh basin was studied in connection with six abiotic environmental parameters (surface flow velocity, width and depth of rivers, connection with the main river, and bottom and maximum temperature). The current species diversity of fish consists of 29 native and 11 alien species. The diversity of right and left tributaries varies greatly as a result of differences in abiotic parameters. The presence of a hydrological connection of reservoirs by itself does not guarantee the distribution of species throughout the basin. Rare indigenous Siberian Taimen Hucho taimen and Markakol Lenok Brachymystax savinovi were regularly found in the right tributaries of the Irtysh River and Lake Markakol, respectively. New fish species to the Kazakh section of the Black Irtysh River have been discovered: Tibetan stone loach Triplophysa stolickai, Severtsov’s loach Triplophysa sewerzowi and alien fish species as asp Leuciscus aspius, Chinese false gudgeon Abbottina rivularis, sunbleak Leucaspius delinetaus, and Misgurnus sp. Full article

Global production of fisheries and aquaculture products continues to increase, with the fisheries sector increasingly considered essential for global food security and nutrition. As public demand for seafood increases, implementation of safety management to minimize risks and ensure the safety of seafood products becomes important. This study was conducted to monitor 198 chemicals, comprising 161 pesticides and 37 pesticide metabolites, and to assess their risks in saltwater and freshwater fish in the Republic of Korea, based on the analysis of 471 fishery samples (298 saltwater and 173 freshwater). Among the fifteen saltwater fish species analyzed, pesticides were detected in eight species (croaker, flatfish, sea bass, flounder, snapper, yellow tail, salmon, and gizzard shad) and in all seven freshwater species (carp, catfish, crucian carp, eel, leather carp, loach, and trout). Four pesticides (ethoxyquin, lufenuron, metaflumizone, and propiconazole) were detected in saltwater fish, while nine pesticides (ethoxyquin, ipfencarbazone, isoprothiolane, lufenuron, metaflumizone, oxadiargyl, pendimethalin, phoxim, and trichlorfon) were found in freshwater fish. Ethoxyquin was the most frequently detected pesticide in both fish types, mostly in the form of its metabolite, the ethoxyquin dimer. The estimated daily intake (EDI) was calculated based on the maximum concentrations of pesticides detected and the average consumption of fishery products by sex and age group. The hazard quotients, expressed as a percentage of acceptable daily intake (%ADI) and calculated using the EDI and ADI of the pesticides detected, were evaluated to be no more than 5.6%. These results suggest that consumption of saltwater and freshwater fish in the Republic of Korea poses a low risk to human health. This approach can be applied to pesticide residue monitoring and risk assessment in the fisheries sector, providing valuable data for evaluating contamination levels and supporting the regulation and management of chemical residues. Full article

The mountainous rivers of Central Asia host diverse ichthyofauna threatened by increasing anthropogenic pressures, particularly water pollution, abstraction, and hydropower development. This study provides valuable morphometric and ecological data for Schizothorax eurycephalus (snow trout) and Triplophysa ferganaensis (stone loach) in the Shakhimardan River basin, Uzbekistan. S. eurycephalus exhibited positive allometric growth, while T. ferganaensis showed negative near-isometric growth. The mean Fulton’s Condition Factor was 1.0 for S. eurycephalus and 0.7 for T. ferganaensis, with site-specific variations. Strong correlations among morphometric parameters, particularly length–height relationships, support non-invasive monitoring techniques. Dietary analysis revealed S. eurycephalus was predominantly herbivorous, with around 70% algae consumption. Early sexual maturity was observed in S. eurycephalus males, whereas T. ferganaensis showed no clear maturity signs, but swollen bellies suggested ongoing or recent reproductive activity. These baseline morphometric and ecological data establish a solid foundation for future ecological assessments, conservation strategies, and the design and monitoring of mitigation measures to address anthropogenic impacts in this vulnerable region. Full article

(1) Background: Polyploid fish are highly important in increasing fish production, improving fish quality, and breeding new varieties. The loach (Misgurnus anguillicaudatus), as a naturally polyploid fish, serves as an ideal biological model for investigating the mechanisms of chromosome doubling; (2) Methods: In this study, tetraploidization in diploid loach was induced by heat shock treatment, and, for the first time, the role of the key cell cycle gene cdk1 (cyclin-dependent kinase 1) in chromosome doubling was investigated; (3) Results: The experimental results show that when eggs are fertilized for 20 min and then subjected to a 4 min heat shock treatment at 39–40 °C, this represents the optimal induction condition, resulting in a tetraploid rate of 44%. Meanwhile, the results of the cdk1 knockout model (2n cdk1^−/−) constructed using CRISPR/Cas9 showed that the absence of cdk1 significantly increased the chromosome doubling efficiency of the loach. The qPCR analysis revealed that knockout of cdk1 significantly upregulated cyclin genes (ccnb3,ccnc, and ccne1), while inhibiting expression of the separase gene espl1 (p < 0.05); (4) Conclusions: During chromosome doubling in diploid loaches induced by heat shock, knocking out the cdk1 gene can increase the tetraploid induction rate. This effect may occur through downregulation of the espl1 gene. This study offers novel insights into optimizing the induced breeding technology of polyploid fish and deciphering its molecular mechanism, while highlighting the potential application of integrating gene editing with physical induction. Full article

This investigation examines the influence of P. dabryanus density on the growth performance of P. nigromaculatus and the structural and functional dynamics of paddy soil microbial communities within a rice–frog–loach integrated aquaculture system. Field experiments were conducted with five density gradients of P. dabryanus (0.5, 1.0, 1.5, 2.0, and 2.5 × 10⁴ individuals/667 m²), designated as RFLS0.5, RFLS1.0, RFLS1.5, RFLS2.0, and RFLS2.5, respectively. Control treatments included rice monoculture (RM) and rice–frog co-culture (RFS). These findings demonstrated that as the density of loach increased, the weight gain ratio of P. nigromaculatus showed a unimodal pattern, reaching its peak in RFLS1. Metagenomic analysis on paddy soil revealed that the RFLS1 facilitated the enrichment of nitrogen-fixing bacteria (Proteobacteria), while concurrently suppressing proliferation of the potential pathogen Pseudomonas aeruginosa and microbial markers in metal-contaminated environments of Usitatibacter rugosus. Further, functional profiling indicated that RFLS1 group reached a peak activity in amino acid metabolism (14.52 ± 0.09%) and carbohydrate metabolism (14.44 ± 0.06%) and showed a higher proportion of glycosyltransferase (GT) abundance (41.93 ± 0.02%) than other groups. In summary, the optimal stocking density of P. dabryanus in rice–frog–loach integrated systems was determined to be 1.0 × 10⁴ individuals/667 m². This density not only promotes the growth of P. nigromaculatus but also improves the structure of paddy soil microbial communities. Full article