Marine Biotechnology最新文献

Microplastics (MPs; less than 5 mm in size) are becoming increasingly prevalent in both terrestrial and aquatic ecosystems. As these particles enter the food chain, they have the potential to pose significant risks to human health. However, their effects on vital fish tissues, such as skeletal muscle, are not yet fully understood. In this study, we examined Nile tilapia (Oreochromis niloticus) from two distinct sites on the Nile River in Egypt: the Nile branch (Damietta branch) and Riah El-Towfiqi. Using Fourier Transform Infrared Spectroscopy (FTIR) and histological study, we confirmed the presence of MPs in both gastrointestinal and muscle tissues. We focused on understanding how MPs might affect fish muscle by investigating the expression of genes involved in muscle atrophy and hypertrophy using Real Time-PCR and histological alterations in muscle tissues of tilapia collected from the two studied sites in the four seasons. Our results revealed histological alterations in muscle tissues collected from the two sites studied in the four seasons. The expression levels of atrophy-related genes, Atrogin-1 (Fbxo32), Capn-1, and the apoptosis marker Caspase3a (Casp3a), showed increased expression, especially during the summer at both sites. On the other hand, the hypertrophy-related gene Igf-1 exhibited a significant decrease while, muscle stem cell genes (Pax3, Pax7) and muscle differentiation gene markers (Myf5, Mrf6) displayed seasonal upregulation, with heightened activity during winter and summer, depending on the location. Additionally, immune-related genes (Ccr9, Irak4, Igl-1, Tlr1) demonstrated notable seasonal changes, with a peak during summer at the Nile branch. These findings demonstrate that MPs can disrupt muscle integrity and immune function in fish, with implications for ecosystem health and potential risks to human food security.

Heterosis refers to the phenomenon in which the progeny resulting from the cross of two parents with different genetic backgrounds exhibit superior traits compared to their parents, such as faster growth rate, higher yield, stronger stress resistance, and better adaptability. In this study, we used the hybrid progeny (150 days of age) of two wild populations of R. philippinarum in northern China (Dalian and Weihai) as samples to preliminarily explore the growth heterosis. In addition, transcriptome sequencing was performed on the hybrid group and the inbred group, showing that there were 2510 DEGs in the DW vs DD groups, 1755 DEGs in the WD vs DD groups, 781 DEGs in the DW vs WW groups, 115 DEGs in the WD vs WW groups, and 582 DEGs in the WD vs DW groups. The MEGF, BMP10, and NOTCH genes play an important role in early development after hybridization. In addition, qPCR results were consistent with RNA-seq data, indicating the reliability of RNA-seq data. Our results provide molecular insights into heterosis.

Single-cycle viruses generated by the deletion of gene(s) essential for viral replication in the genome can be a way to enhance the safety of attenuated virus-based vaccines because single-cycle viruses can infect cells only once and cannot produce infective viral particles. In the present study, not only to guarantee safety as a prophylactic vaccine but also to enhance the protective efficacy, a single-cycle viral hemorrhagic septicemia virus (VHSV) lacking the G gene and containing olive flounder (Paralichthys olivaceus) interferon-γ (IFNγ) ORF between N and P genes of the viral genome (rVHSV-A-IFNγ-ΔG) was rescued using reverse genetic technology, and its protective potential was evaluated through the immunization of olive flounder. In the challenge experiment, the cumulative mortality in the control group reached 80%, while groups of fish immunized with various doses of rVHSV-A-IFNγ-ΔG (ranging from 1 × 10³ to 1 × 10⁵ pfu/fish) showed no mortalities. In contrast, fish immunized with various doses of rVHSV-ΔG exhibited 0–20% mortality in a dose-dependent manner. Serum ELISA analysis revealed that groups receiving the highest doses of rVHSV-ΔG and rVHSV-A-IFNγ-ΔG showed significantly elevated titers compared to the control group. Although no statistically significant differences in ELISA titers were observed among groups immunized with lower doses of recombinant VHSVs, particularly at 1 × 10³ pfu/fish, and the control group, the markedly higher protection compared to the control group suggests that these single-cycle viruses possess a limited capacity to induce antibody responses, yet are capable of conferring protective immunity against VHSV independently of humoral mechanisms. Moreover, the complete protection achieved with low-dose immunization of rVHSV-A-IFNγ-ΔG indicates its strong potential as a highly effective prophylactic vaccine candidate.

In diploid organisms, deleterious recessive alleles represent a significant component of genetic mutations and often result in lethal effects when in a homozygous state. Large yellow croaker (Larimichthys crocea), a critical marine aquaculture species in China, has shown signs of inbreeding depression due to its limited natural distribution along the coasts of Fujian, Guangdong, and Zhejiang provinces, combined with intensive artificial propagation practices. Identifying loci with deleterious recessive homozygous genotypes is therefore crucial for sustainable industry development. In this study, 1844 large yellow croaker across three consecutive generations were analyzed, resulting in the preliminary identification of 131 loci with missing recessive homozygous genotypes. After excluding false positives through parentage analysis, large-scale validation was conducted using genotype data from 4663 individuals from the MinDong population and 830 individuals from the Daqu population. Ultimately, 22 loci with complete absence of homozygous recessive genotypes were identified across 7337 individuals. The average minor allele frequency (MAF) of these loci was 0.16. Except for LG17_2296176 and LG17_4414232, which exhibited moderate linkage disequilibrium, the remaining 20 loci were largely independent with no observed linkage disequilibrium. Annotation of the 22 loci identified 12 associated genes, including vegfa, sntg2, tcf7, kif2a, lage3, ano10, mpdu1, and others. These genes are involved in key biological processes such as signal transduction regulation, cytoskeletal organization, neural function, and glycan synthesis. To further verify the reliability of the loci with missing recessive homozygous genotypes, heterozygous parental fish carrying 6 randomly selected loci were paired to establish independent families. None of the offspring exhibited recessive homozygous genotypes at these loci, supporting the accuracy of the prior identification. By analyzing genotype data from large yellow croaker populations, this study identifies key loci with missing recessive homozygous genotypes. These findings may offer guidance for selective breeding strategies aimed at minimizing lethal mutations, thereby enhancing population fitness and supporting the sustainable development of the aquaculture industry.

The fillet yield phenotype is a trait that can be improved in aquaculture species through conventional selective breeding. This approach was applied to rainbow trout for three consecutive generations of selection to produce a high-yield line (HY) that exhibits 2.5 percentage points higher fillet yield compared to a low-yield line (LY). To characterize the genetic and physiological mechanisms contributing to the HY phenotype, transcriptomic analysis of liver and skeletal muscle was performed at three stages of development, 2 g, 60 g, and 300 g, which corresponded to 35, 208, and 277 days post-hatch. Functional analysis of differentially expressed genes (DEG) suggests that increased muscle yield in the HY line is partially driven by greater hyperplasia at 60 g; although, higher rates of protein accretion, primarily attributed to lower rates of protein degradation, promote muscle cell hypertrophy during all stages of development. Additionally, DEGs support reductions in glycolysis in the HY muscle, with increased activity of the more efficient citric acid cycle and oxidative phosphorylation reactions for energy production compared to the LY line. In the liver, DEGs indicate unique nutrient utilization mechanisms in the HY line that support reduced visceral adiposity compared to the LY line. These findings provide insight into the physiology and metabolism driving the high fillet yield phenotype; this information is useful for the development of genomic markers to enhance breeding strategies toward the improvement of performance traits.

Marine fungi have been receiving increasing interest, especially with respect to their potential for biotechnological applications. Carbon sources in marine environments, such as seaweeds, have cell walls that are structurally different from the cell walls of terrestrial plants, which implies that marine fungi likely possess a specific set of extracellular enzymes to enable them to use these marine substrates as carbon and energy source. In addition, marine fungi have been implicated as good sources of secondary metabolites with bioactive functions, as e.g., drugs and antibiotics. To evaluate if marine fungi have genomic signatures that distinguish them from terrestrial fungi with respect to biotechnological potential, we genome-sequenced three marine fungal species (Varicosporina prolifera, Corollospora maritima, Emericellopsis maritima), two terrestrial species (Clonostachys rosea, Stanjemonium grisellum), and one that is found in both terrestrial and marine environments (Microascus triganosporus) and compared them to taxonomically-related terrestrial (Microascus stellatus, Valetoniellopsis laxa) and marine species (Emericellopsis atlantica) for which genomes were already available. These fungi originate from two orders (Microascales, Hypocreales) of the Sordariomycetes. We then compared their carbohydrate-active enzymes and secondary metabolism content and their ability to use terrestrial and marine biomass as carbon sources. The analysis revealed that despite the presence of some genes specific to marine fungi, no general genomic or growth phenotypes can be identified to distinguish marine fungi from terrestrial fungi, suggesting that all have maintained the ability to use both marine and terrestrial carbon sources.

Spermatogenesis is a complicated process of sexual reproduction, involving cell proliferation and differentiation, and depends on intricate interactions between testicular somatic cells and germ cells. For further investigations on male germ cells’ development and differentiation in Chinese soft-shelled turtle (Pelodiscus sinensis), it is crucial to define testicular cell types and their molecular regulators. Here, the 10 × Genomics single-cell RNA sequencing was adopted to study the transcriptomic profiles of single cells during the spermatogenesis of adult Chinese soft-shelled turtle. In total, 7317 individual cell transcriptomes were collected for analysis, and 11 cell types were identified with known differentially expressed genes, including Leydig cells, Sertoli cells, spermatogonia, spermatocytes, and spermatids. Likewise, the top 10 marker genes and top-enriched gene pathways were analyzed in each cell type. Intriguingly, ligand-receptor analysis showed that the strongest interaction between Leydig cells and germ cells was using CellChat. Moreover, a primary developmental trajectory of male germ cells was constructed from spermatogonia to spermatids, as well as some important cell-specific regulators were identified for labeling the germ cells at different stages, including PCNA and Stra8, validated by immunostaining fluorescence. In addition, the transcriptomic profiles of male germ cells at different stages were comparatively analyzed among fruit fly, fish, mammals, and Chinese soft-shelled turtle, and the conserved and divergent regulators of male germ cells were summarized across species. In conclusion, this study provided novel insights into the testicular cells’ atlas in turtles, and the findings would facilitate the development of techniques for manipulating germ cells, such as isolating cells and defining stages of differentiation.

Berberine hydrochloride (BH), the derivative component of Coptidis chinensis, is widely used to treat bacterial infections due to its notable antibacterial properties. However, the underlying molecular mechanisms of its therapeutic effects remain largely unexplored. This study employed transcriptome sequencing to investigate berberine hydrochloride's therapeutic efficacy and molecular responses in Branchiostoma belcheri infected with Aeromonas hydrophila. In this study, B. belcheri was first exposed to 200 mg/L berberine hydrochloride (BH) for 24 h, and then infected with A. hydrophila. After 48 h, transcriptome differential expression analysis was performed to compare the transcriptomic changes with the control group. A total of 2,478 differentially expressed genes (DEGs) were identified. Enrichment analysis revealed that these DEGs are involved in key pathways such as metabolism, cellular processes, signal transduction, and immune functions. Berberine hydrochloride treatment activated pathways including retinol metabolism, proteasome function, oxidative phosphorylation, lysosome, phagosome, and glutathione metabolism. RT-PCR validation confirmed the upregulation of immune-related genes such as TUBA, RAB5A, CTSL, GST, GPX4, G6PD, ND1, COX2, FECH, and LYP3A across these seven pathways. Notably, the glutathione metabolism, phagocytosis, and oxidative phosphorylation pathways appear to be central in regulating BH-mediated protection against A. hydrophila infection in B. belcheri. Moreover, BH significantly enhanced the activity of glutathione-related pathways, including GST, GSH, GPX, and GSSG in the hepatic caecum, activating oxidative defence systems and modulating immune-related responses in B. belcheri under A. hydrophila exposure. These results provide new insights into the potential role of BH in enhancing immune and oxidative stress responses in lancelets, which may have implications for its application in aquaculture.

Graphical Abstract

The hard-shelled mussel (Mytilus coruscus), a commercially vital bivalve in China, accumulates lipids predominantly in its gonads, the species’ primary edible tissue. Understanding the molecular mechanisms underlying gonad-specific lipid storage is critical for improving reproductive efficiency and aquaculture yield. This study employs comparative transcriptomic analysis of multiple tissues (gonad, gill, mantle, foot, hemolymph) to pinpoint key regulatory genes involved in lipid deposition. Through weighted gene co-expression network analysis (WGCNA), vitellogenin (VG), perilipin (PLIN), and transmembrane protein (TM) were identified as hub genes in gonadal lipid regulation. Genomic characterization revealed 13 VG and three PLIN family members in M. coruscus, which displayed conserved structural motifs and were syntenic with related bivalves, underscoring their functional significance. Phylogenetic analyses further highlighted the evolutionary conservation of these lipid-associated genes across marine invertebrates. Concurrently, sex-specific metabolic divergence was investigated. Physiological validation demonstrated that ovarian crude fat content exceeded testicular levels by 36%, corroborated histologically by larger, more stable lipid droplets in female gonads. Sex-specific expression profiling uncovered pronounced divergence: VG and PLIN were markedly enriched in ovaries, whereas glucose-6-phosphatase (G6P), a driver of energy catabolism, was elevated in testes. This study provides a molecular framework for understanding reproductive lipid metabolism in bivalves, offering biomarkers to refine broodstock management and aquaculture practices.

The orange-spotted grouper (Epinephelus coioides) is an economically important marine species in the South China Sea. Due to overfishing and environmental pollution, its natural resources in the South China Sea have severely declined. Evaluation of genetic diversity of the orange-spotted grouper in the distribution areas is important for future conservation action. In this study, a molecular marker specific for orange-spotted grouper E. coioides was developed based on the mitochondrial D-loop region sequences. We evaluated the community structure and genetic diversity of the groupers at four stock enhancement sites of the Wanshan Archipelago by employing integrated assessment methods including environmental DNA (eDNA) and the D-loop marker. Five grouper species were identified from the eDNA samples using 12S rDNA metabarcoding technology, with the orange-spotted grouper being the most abundant grouper ranging from 39.05% to 49.79% of the grouper contents. Furthermore, 15 D-loop haplotypes for the orange-spotted grouper in the Wanshan Archipelago release areas were detected by utilizing the novel developed D-loop marker. High haplotype genetic diversity was observed at all sampling sites for the orange-spotted grouper population. Dominant haplotypes such as ASV_1, ASV_2, ASV_3, ASV_4, and ASV_5 exhibited high levels of geographic sharing, suggesting a degree of ecological or environmental similarity across these regions. Most of the genetic variations were originated within populations, indicating significant genetic differentiation among grouper populations in the Wanshan Archipelago. Our study indicates that eDNA technology is a valuable non-invasive tool for monitoring fish community structure, and the haplotype diversity of E. coioides in the sampled waters maintained a relatively high haplotype richness.