The green microalgae Oocystis borgei has remarkable potential for improving aquaculture water quality, particularly in terms of dissolved nitrogen. However, the mechanisms underlying nitrogen assimilation in this species remain poorly understood. The glutamine synthase (GS2) gene plays a crucial role in the nitrogen metabolism pathway in plants. To accurately reflection GS2 expression levels in O. borgei under abiotic conditions, it is essential to select stable reference genes for qPCR analysis. This study assessed the expression stability of nine reference genes (EF1 alpha, RPL7, UBCE, GAPDH, 18S, rbcL, beta-TUB, UBQ, and RPS27) of O. borgei under five abiotic conditions (temperature, light intensity, salinity, nitrogen concentration, and carbon concentration) based on the analysis results calculated by the four algorithms of Delta Ct, GeNorm, NormFinder, and BestKeeper, which were ranked by ReFinder. The results demonstrated that EF1 alpha and UBCE for temperature treatment, UBCE and RPS27 for light intensity and salinity treatment, RPS27 and RPL7 for nitrogen concentration treatment and the pooled sample, and UBCE and UBQ for carbon concentration treatment were the ideal reference genes combination for O. borgei, respectively. Additionally, the relative expression levels of GS2 under different abiotic conditions was detected and compared to verify the validity of selected reference genes and the results showed that the expression of GS2 in O. borgei was significantly affected by all experimental factors. Our study was helpful to acquire the accurate data of nitrogen assimilation related gene expression during aquaculture water quality control based on microalgae.

Clarias fuscus, renowned for its resilience and nutritional value, is a significant aquaculture species in China. To facilitate further genetic research and breeding programs in this species, we generated an improved high-quality chromosome-level genome assembly of a female C. fuscus using MGI, PacBio, and Hi-C sequencing technologies. The final genome assembly spans 982.84 Mb, with contig and scaffold N50 values of 36.16 Mb and 37.66 Mb, respectively, and successfully anchors 99.60% of the sequences to 28 pseudochromosomes. We also predicted 24,849 protein-coding genes, with 97.3% of them functionally annotated. BUSCO analysis indicates a completeness of 97.03% for the assembly and 96.6% for the annotation. This study significantly advances the genomic resources available for C. fuscus and supports future molecular breeding and functional genomics research.

Hemoglobin (Hb) plays a pivotal role in oxygen transport and is essential for the adaptive response to hypoxic stress. Studying the molecular evolution characteristics and expression pattern of S. sihama Hb gene family can provide theoretical basis for further revealing the roles of the Hb genes against hypoxia stress. This study aimed to identify the molecular evolution characteristics and expression patterns of Hb genes in S. sihama. Utilizing bioinformatics methods, we identified ten members of the Hb gene family within the whole genome of S. sihama, located on chromosomes LG16 and LG21 in a tandem repeat pattern. Phylogenetic analysis classified the Hb gene family into two subfamilies (alpha and beta), showing close relationships with the Hb gene family members of the large yellow croaker (Larimichthys crocea). Both phylogenetic and collinearity analysis indicated the conservation of Hb genes throughout evolution. The nonsynonymous substitution rate / synonymous substitution rate (Ka/Ks) results showed that its evolution was purifying selection. RNA-seq and qRT-PCR analyses revealed that five Hb genes were highlighted high expression levels in the heart and liver of S. sihama, with sshba1.4, sshbad, and sshba1 showing significant up-regulation in response to hypoxic stress. In summary, this study highlights the vital role of the Hb gene family in the hypoxic stress response of S. sihama, suggesting their potential as crucial candidate genes for regulating environmental stress in this species.

In order to investigate the effects of various nitrogen (ammonium) concentrations on the epibiotic bacterial community associated with Oocystis borgei, a metabarcoding sequencing method was employed. The 16S rDNA sequencing and bioinformatic analysis were conducted on cultures of O. borgei that were grown on four different nitrogen element concentrations (2.5, 10, 50, and 100 mg/L), and the differences in the epibiotic bacterial community and functions of O. borgei among different nitrogen concentrations were compared. The results showed that the chlorophyll a content of O. borgei increased with increasing nitrogen concentrations. A total of 43 operational taxonomic units (OTUs) were obtained from the four groups, which were categorized into 7 phyla, 9 classes, 18 orders, 21 families, and 26 genera. Winogradskyella was the dominant genus in the groups with 2.5 and 100 mg/L nitrogen, while Marinobacter and Winogradskyella were relatively abundant in the groups with 50 and 100 mg/L nitrogen. Functional analysis using PICRUST2 showed that the three most abundant gene functions were carbohydrate metabolism, amino acid transport and metabolism, ribosomal structure and biogenesis, and energy production and conversion. BugBase phenotypic analysis revealed that there were no significant differences in phenotypes between the groups with 2.5 and 10 mg/L nitrogen, while the group with 50 mg/L nitrogen exhibited higher abundance in aerobicity, biofilm formation, mobile genetic elements, and stress tolerance phenotypes. Most of the bacteria in this work belonged to the aerobic types. A redundancy analysis (RDA) of environmental factors demonstrated that nitrogen concentration showed a positive correlation with species changes in the groups with 10 and 50 mg/L nitrogen; chlorophyll a exhibited a positive correlation with species changes in the groups with 50 and 100 mg/L nitrogen. Nitrogen concentration significantly influenced the epibiotic bacterial community associated with O. borgei, leading to changes in dominant species and community structure. This study provides important references for understanding the functional characteristics of the epiphytic microbial community of O. borgei and the exploration of specific microorganisms.

Global climate change has a significant impact on fish survival and the aquaculture industry. Even highly adaptable organisms like Siluriformes fish are susceptible to these effects. This study investigates the consequences of extreme high temperature on Hong Kong catfish (Clarias fuscus), a species known for its long-term habitation in tropical and subtropical regions. In this study, C. fuscus were cultivated for 90 days at high temperature (HT, 34 degrees C) and normal temperature (NT, 26 degrees C), followed by subjecting the two groups to high temperature stress (34 degrees C) and temperature recovery (26 degrees C). The hepatic histology, biochemical, and transcriptomic characteristics of the species were examined before acute high temperature stress (NT-C, HT-C), after acute high temperature stress (NT-T, HT-T), and after temperature recovery (NT-R, HT-R). The histological analysis revealed that long-term heat stress damaged the liver tissue of C. fuscus. Furthermore, significant damage was observed in the liver tissues of the NT group under acute high temperature stress, while no further damage was observed in the HT group. The biochemical analysis showed that 90 days of heat stress altered the body's immune and oxidative balance, resulting in an increase in alkaline phosphatase (ALP), alanine aminotransferase (ALT), catalase (CAT), superoxide dismutase (SOD) and glutathione peroxidase (GPX) activities, and a decrease in malondialdehyde (MDA) content. Upon acute heat stress, the liver function of the NT group was disordered and unable to produce enough total-bilirubin (T-BIL), while the aspartate aminotransferase (AST) activity of the HT group was more susceptible to being affected. Long-term heat stress led to significant changes in gene expression, with the NT group showing three times more differentially expressed genes (DEGs) identified in the liver compared to the HT group under acute heat stress conditions. Analysis of DEG enrichment during the same treatment period in both groups revealed significant differences in amino acid metabolism and lipid metabolism pathways. These results suggest that long-term heat stress caused liver tissue damage in C. fuscus, altering immune and oxidative balance, enzyme activity sensitivity, as well as the body's response to acute heat stress pathways and intensity. This study lays the groundwork for future investigations into fish adaptability to sudden temperature changes and aquaculture strategies to mitigate heat stress in fish facing extreme temperatures.

Due to the non-degradable and persistent nature of metal ions in the environment, they are released into water bodies, where they accumulate in fish. In order to assess pollution in fish, the enzyme, glucose 6-phosphate dehydrogenase (G6PD), has been employed as a biomarker due to sensitivity to various ions. This study investigates the kinetic properties of the G6PD enzyme in yellow catfish ( Pelteobagrus fulvidraco ), and analyzes the effects of these metal ions on the G6PD enzyme activity in the ovarian cell line (CCO) of channel catfish ( Ictalurus punctatus ). IC 50 values and inhibition types of G6PD were determined in the metal ions Cu 2+ , Al 3+ , Zn 2+ , and Cd 2+ . While, the inhibition types of Cu 2+ and Al 3+ were the competitive inhibition, Zn 2+ and Cd 2+ were the linear mixed noncompetitive and linear mixed competitive, respectively. In vitro experiments revealed an inverse correlation between G6PD activity and metal ion concentration, mRNA levels and enzyme activity of G6PD increased at the lower metal ion concentration and decreased at the higher concentration. Our findings suggest that metal ions pose a significant threat to G6PD activity even at low concentrations, potentially playing a crucial role in the toxicity mechanism of metal ion pollution. This information contributes to the development of a biomonitoring tool for assessing metal ion contamination in aquatic species.

Hong Kong catfish (Clarias fuscus) is a valuable fish species widely farmed in southern China, showing distinct differences in growth between males and females. Studying gene expression patterns during gonadal development in C. fuscus is essential for uncovering the genetic basis of sex variances and guiding breeding practices. This research presents a detailed analysis of gene expression during Phases II, III, and IV of gonadal development. A total of 11,948, 7145, and 10,672 differentially expressed genes (DEGs) were identified at these stages, with 4253 DEGs common across all three phases. Key genes related to gonadal development were pinpointed, showing significant sex-specific expression during testes or ovaries development. These genes included those involved in steroid synthesis (cyp17a1, cyp11a1, hsd3b1, cyp26a1, hsd17b12), transcription factors (sox9a, lhx9, sox19b), and TGF-β superfamily genes (tgfb2, amh, bmp15, gdf9). Additionally, genes exclusively expressed during gonadal development were identified, such as dmrt1l, cyp26c1, hsd3b1l, six2b, foxj1a, cfap65, and cfap43 in testes, and sox2, zp3, mos in ovaries. KEGG enrichment analysis highlighted the importance of the Fanconi anemia pathway in oocyte meiosis and ovarian development in C. fuscus. Furthermore, weighted gene co-expression network analysis (WGCNA) emphasized the role of pathways like progesterone-mediated oocyte maturation, oocyte meiosis, and steroid hormone biosynthesis in gonadal development. This study identified crucial genes and pathways involved in the gonadal development of C. fuscus, setting the stage for a deeper understanding of the molecular mechanisms behind sex differentiation and reproductive development.

Oxygen is vital for the survival, growth, development, and reproduction of organisms. This study investigates the genetic basis of hypoxia tolerance in the silver sillago ( Sillago sihama ), a species highly valued in aquaculture despite its traditional susceptibility to low oxygen environments. By employing quantitative trait locus (QTL) mapping and single nucleotide polymorphism (SNP) association studies, the study enhances our comprehension of the genetic factors involved in hypoxia tolerance. Six QTLs associated with hypoxia tolerance have been identified, spanning five distinct linkage groups. Enrichment analyses highlighted important biological processes and pathways, particularly those related to potassium ion transport and cytochrome P450 -mediated drug metabolism, which play a critical role in responding to hypoxia stress. Seven candidate genes have been identified as relevant to hypoxia tolerance: cyp20a1, mgst3b, kcnh2, cluh, adk, xdh, and slc19a2 . Notably, the SNP association analysis has identified 13 SNPs within the mgst3b gene, with five SNPs ( g.583 T > C, g.611 A > G, g.629 T > A, g.633 T > A, g.937 A > G ) showing a significant association with hypoxia tolerance. This study sheds light on the molecular mechanisms underlying hypoxia tolerance and suggests potential genetic markers that could be used to enhance S. sihama ' s ability to withstand hypoxic conditions through selective breeding, providing valuable insights for the improvement of sustainable aquaculture practices.

Alexandrium pacificum（A.pacificum） is a typical paralytic shellfish poisonous dinoflagellate.Harmful algal blooms（HABs）caused by this species can bring serious environmental problems and economic losses to the aquaculture industry.In this study,transcriptome sequencing and analyses were performed on the neural tissue of Litopenaeus vannamei（L.vannamei） after acute exposure to A.pacificum disrupted solution for 72 h,and differentially expressed genes（DEGs） were identified.The results showed that,compared with the control samples,300 DEGs were identified in the experimental group,of which 194 were up-regulated,and 106 down-regulated.The gene ontology（GO） functional enrichment analysis showed that DEGs were significantly enriched in the cortical cytoskeleton organization,troponin complex,amylo-alpha-1,6-glucosidase and thymidine phosphorylase.Kyoto encyclopedia of genes and genomes（KEGG） enrichment analysis found that DEGs were mainly enriched in the oxidative phosphorylation process,intercellular tight junctions and mitophagy.The results showed that the proteoglycans,signaling pathways,and various metabolic processes that regulate cell proliferation,differentiation,and apoptosis all played an essential role in the response of L.vannamei to A.pacificum toxins.

The giant freshwater prawn (Macrobrachium rosenbergii) is a commercially valuable freshwater crustacean species that frequently appears a death affected by various diseases, resulting in substantial economic losses. Improving the survival rate of M. rosenbergii is a hot and essential issue for feeding the prawns. Scutellaria polysaccharide (SPS) extracted from Scutellaria baicalensis (a Chinese medicinal herb) is conducive to the survival rate of organisms by enhancing immunity and antioxidant ability. In this study, M. rosenbergii was fed 50, 100, and 150 mg/kg of SPS. The immunity and antioxidant capacity of M. rosenbergii were tested by mRNA levels and enzyme activities of related genes. The mRNA expressions of NF-κB, Toll-R, and proPO (participating in the immune response) in the heart, muscle, and hepatopancreas were decreased after four weeks of SPS feeding (P < 0.05). This indicated that long-term feeding of SPS could regulate the immune responses of M. rosenbergii tissues. The activity levels of antioxidant biomarkers, alkaline phosphatase (AKP), and acid phosphatase (ACP) had significant increases in hemocytes (P < 0.05). Moreover, catalase (CAT) activities in the muscle and hepatopancreas, as well as superoxide dismutase (SOD) activities in all tissues, significantly decreased after four weeks of culture (P < 0.05). The results demonstrated that long-term feeding of SPS could improve the antioxidant capacity of M. rosenbergii. In summary, SPS was conducive to regulating the immune capacity and enhancing the antioxidant capacity of M. rosenbergii. These results provide a theoretical basis for supporting SPS addition to the feed of M. rosenbergii.

BackgroundHong Kong catfish (Clarias fuscus) is an ecologically and economically important species that is widely distributed in freshwater regions of southern China. Hong Kong catfish has significant sexual growth dimorphism. The genome assembly of the Hong Kong catfish would facilitate study of the sex determination and evolution mechanism of the species.ResultsThe first high-quality chromosome-level genome of the Hong Kong catfish was constructed. The total genome was 933.4 Mb, with 416 contigs and a contig N50 length of 8.52 Mb. Using high-throughput chromosome conformation capture (Hi-C) data, the genome assembly was divided into 28 chromosomes with a scaffold N50 length of 36.68 Mb. A total of 23,345 protein-coding genes were predicted in the genome, and 94.28% of the genes were functionally annotated in public databases. Phylogenetic analysis indicated that C. fuscus and Clarias magur diverged approximately 63.7 million years ago. The comparative genome results showed that a total of 60 unique, 353 expanded and 851 contracted gene families were identified in Hong Kong catfish. A sex-linked quantitative trait locus identified in a previous study was located in a sex-determining region of 30.26 Mb (0.02 to 30.28 Mb) on chromosome 13 (Chr13), the predicted Y chromosome. This QTL region contained 785 genes, of which 18 were identified as sex-related genes.ConclusionsThis study is the first to report the chromosome-level genome assembly of Hong Kong catfish. The study provides an excellent genetic resource that will facilitate future studies of sex determination mechanisms and evolution in fish.

Olfactory receptor (OR) genes are essential in the specific recognition of diverse stimuli in fish. In this study, a total of 141 OR genes were identified in silver sillago (Sillago sihama), a marine fish sensitive to environmental stimuli, including 112 intact genes, 26 truncated genes, and three pseudogenes. A phylogenetic tree analysis elucidated that the OR genes of S. sihama were classified into six groups, of which β, γ, δ, ε, and ζ groups belonged to type I, and the η group belonged to type II. The type I OR genes contained almost all conserved motifs (n = 62), while type II OR genes mainly retained conserved motifs 7(3), 1, 10, 4, and 2 (n = 39). OR genes were mainly distributed on LG1, LG9, LG11, and LG12. Of all OR genes, 36.23% (50 genes) showed significant expansion in S. sihama. Ka/Ks analysis demonstrated that 227 sites were under purifying selection, while 12 sites were under positive selection, including eight genes in the OR2A12 gene subfamily. Sixty-one genes (44.20%) displayed differential expression under hypoxic stress. The identified OR genes explored the mechanism of environmental stress and ecological adaptation of S. sihama, and provided valuable genomic resources for further research on the olfaction of teleosts.

DATA REPORT article Front. Genet., 17 October 2023Sec. RNA Volume 14 - 2023 | https://doi.org/10.3389/fgene.2023.1255595

Microalgae serve as feedstock for bivalves and larvae in aquaculture. The production of microalgae in large quantities is, however, characterized by the high cost of major nutrients and vitamins and scarcity of freshwater. Wastewater is a cheap alternative medium for microalgae cultivation. The wastewater provides essential nutrients for microalgae growth and biomass production. This study examined the biomass productivity, nutrient removal, and biochemical content of Chlorella vulgaris, Spiruna platensis, and Haematococcus pluvialis biomass cultivated in membrane treated distillery wastewater (MTDW). The study further examined the use of cultivated biomass as a diet to analyze the growth and survival rate of Pinctada fucata martensii. The results showed 79.61% and 82.89%, and 41.73% of Total Nitrogen (TN) and 74.95%, 78.21%, and 29.05% of Total Phosphorus (TP) removal efficiency for C. vulgaris, S. platensis, and H. pluvialis respectively. Biomass productivity of 0.069 g L−1, 0.086 g L−1, and 0.057 g L−1, 43.3%, 40.9%, and 34.9% (protein), 10.3%, 14.5%, and 13.8% (lipid), and 16.4%, 14.8%, and 20.8% (carbohydrate) for C. vulgaris, S. platensis, and H. pluvialis respectively. The specific growth rate and survival rate of pearl oysters were significantly (p < 0.05) higher (0.99 ± 0.12%, 87.3%) under C. vulgaris diet compared to S. platensis and H. pluvialis diets.

AbstractDielectric materials with excellent energy storage performance are urgently needed in advanced electrical power systems. We have reported that Mn2+‐doped SrTiO3 thin films have high energy storage density. However, the thin films exhibit fat polarization‐electric field hysteresis loops with high hysteresis, which is not conducive to greater energy storage performance. In this work, the Ca2+‐doped Sr1‐xCaxTi0.99Mn0.01O3 thin films are fabricated to construct slim polarization‐electric field hysteresis loops with low hysteresis for obtaining excellent energy storage performance. Because Ca2+ can break the long‐range ferroelectric order of SrTi0.99Mn0.01O3, the domain size decreases and the coupling of domains weakens, ultimately leading to low hysteresis. Moreover, doping Ca2+ can induce distortion of the octahedral [TiO6] to form local polarization regions. When doped an appropriate amount of Ca2+, local lattice distortion plays an important role in polarization behavior, which helps to enhance polarization. Meanwhile, the Ca2+‐doped thin films also possess good insulation. Finally, the higher energy storage density of 63.9 J cm‐3 is achieved in the Sr0.9Ca0.1Ti0.99Mn0.01O3 thin film. When the electric field is less than 4000 kV cm‐1, the energy storage efficiency remains above 70%. Simultaneously, a wide working temperature range from ‐100℃ to 100℃ is also obtained.

Hong Kong catfish (Clarias fuscus) is a freshwater fish that has economic value and is widely cultured in southern China. C. fuscus has significant sexual growth dimorphism. In this study, full-sib F1 individuals of C. fuscus were used as a mapping family to construct a high-density genetic linkage map, and sex-related quantitative trait loci (QTL) were mapped using single nucleotide polymorphism (SNP) markers by restriction-site associated DNA sequencing (RAD-seq) technology. The genetic map was divided into 28 linkage groups with a total map distance of 4870.15 cM, 6453 markers, and an average genetic distance of 0.75 cM between markers. Based on the genetic linkage map, interval mapping was performed to identify sex-related QTLs. A sex-related QTL, qSEX-1, was successfully mapped to LG13, which contained 225 linked SNP markers. The LOD value for the main QTL peak was 77.18, located at 138.32 cM, and the proportion of phenotypic variance explained (PVE) for sex was 83.1%. A candidate sex-determination region was identified within the qSEX-1 interval, with a total map distance of 16.073 cM and 15 SNP markers. The np544 marker was highly linked to sex. In summary, the first genetic linkage map of C. fuscus was generated based on high-throughput sequencing. Moreover, sex-linked SNP loci and a sex-determining interval were identified, providing methodological guidance and important tools for sex control technology in C. fuscus breeding.

The dietary supplementation of Haematococcus pluvialis is a natural, safe, and sustainable method for fish pigmentation. However, astaxanthin-rich H. pluvialis cysts have a poor effect in pigmenting salmonid flesh due to their rigid and thick cell wall. H. pluvialis thin-walled motile cells have recently attracted attention due to their potential advantages in maintaining compound stability, easy digestion, enhancing the bioavailability of carotenoids, and reducing production costs. This study aimed to investigate the effect of various nitrogen concentrations and light intensities on astaxanthin production in motile cells. We first investigated the effect of four different concentrations of nitrogen on astaxanthin accumulation in motile cells. According to the results, the motile cells had the highest astaxanthin concentration and content under the 0 N condition. Then, we compared the differences in astaxanthin production in motile cells under three different light intensities under 0 N conditions. The results showed that after four days of treatment, the protoplasts of the motile cells in the medium light (ML) group and the high light (HL) group had distinct granularity. The cell mortality rate in the HL group reached more than 15%, which was significantly higher than that in the low light (LL) and ML groups, indicating that high light intensity was not suitable for inducing motile cells to accumulate astaxanthin. There were no significant differences between the LL and ML groups in astaxanthin content, motile cells percentage, and cell mortality rate. Considering these indicators, we recommended inducing motile cells to produce astaxanthin under low light conditions because it is more economical in terms of electricity consumption. This study added to the knowledge that nitrogen and light affects the accumulation of astaxanthin in H. pluvialis motile cells. The results would help determine the optimal nitrogen and light conditions in astaxanthin production from motile cells.

Glutathione S-transferase (GST) is an important detoxification enzyme in organisms. GSTs play an important role in responding to environmental stresses. This study aimed to identify the GST gene superfamily in silver sillago (Sillago sihama) and analyze its expression pattern under hypoxia stress. A total of 17 GST genes were identified in silver sillago. Phylogenetic analysis showed that the GST gene family contained two subgroups (cytosolic and MAPEGs), and lacked three subgroups (i.e. Pi, Kappa, and MGST2). Phylogenetic and syntenic analysis revealed that GST genes were conserved in evolution. Eight SsGSTs were significantly differentially expressed under hypoxia stress in silver sillago by RNA-seq and qRT-PCR analysis. The expression levels of SsMGST3b, SsGSTO1, SsGSTT1b and SsGSTR2 genes were significantly up-regulated after 4 h of reoxygenation in the gill tissue. In the heart tissue, the expression of SsGSTR3 was significantly up-regulated after 1 h of hypoxia while the expression levels of SsGSTT1b and SsFLAP genes were significantly down-regulated after 4 h of hypoxia. In summary, this study provides for the first time a comprehensive analysis of the GST gene superfamily of silver sillago.

The alcohol industry discharges large quantities of wastewater, which is hazardous and has a considerable pollution potential. Cultivating microalgae in wastewater is an alternative way of overcoming the current high cost of microalgae cultivation and an environmentally friendly treatment method for industrial effluents. The study analyzed the growth and biochemical composition of Chlorella vulgaris cultivated in membrane-treated distillery wastewater (MTDW) and nutrients removal efficiency. The results showed biomass productivity of 0.04 g L −1 d −1 for MTDW with the contents of content of protein, carbohydrate, and lipid at 49.6 ± 1.4%, 26.1 ± 0.6%, and 10.4 ± 1.8%, respectively. The removal efficiencies of TN, TP, and COD were 80, 94, and 72.24% in MTDW, respectively. In addition, removal efficiencies of 100, 85.37, and 42.86% for Ca 2+ , Mg 2+ , and Mo 2− were achieved, respectively. The study added to our growing knowledge on the cultivation of Chlorella with wastewater, suggesting that it was feasible to cultivate Chlorella with MTDW and represented an economical and environmentally friendly strategy for microalgae biomass production and reuse of wastewater resources.