Marine Biotechnology最新文献

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.

The mandarin fish (Siniperca chuatsi) is a significant freshwater aquaculture species in China, exhibiting sexual dimorphism during growth. However, the cellular and molecular mechanisms underlying early gonadal development and sex differentiation remain unclear. This study traces early gonadal development by examining changes in gonadal histology, germ cell morphologic and distributional changes, and the expression of key signaling molecules. H&E staining and immunofluorescence analysis revealed that oogonia and spermatogonia first appeared at 27 and 33 days post-fertilization (dpf), respectively, marking the onset of sex differentiation. By 51 and 57 dpf, oocytes and spermatocytes became more abundant, indicating the completion of sex differentiation. We examined the expression of female-biased (cyp19a, dmrt2 and foxl2a), male-biased (amh, dmrt1, gsdf and sox9), and meiotic genes (dmc1 and sycp3). In male gonads, the expression of amh was detected at 21–42 dpf, and it showed significantly higher expression after 42 dpf compared to females. Meanwhile, the expression of dmrt1 was significantly higher in male gonads than in female gonads at 30 to 33 dpf. The dmrt3 gene had high expression levels in both male and female gonads before 45 dpf, with a further increase observed after 51 dpf. The gsdf gene exhibited higher expression levels in male gonads between 27 and 42 dpf than at other time points. Additionally, Sox9 expression was significantly higher levels observed in males than in females at 33 dpf. In female gonads, cyp19a was consistently expressed from 21 to 42 dpf and was significantly higher than that in males after 42 dpf, dmrt2 expression was higher than that in males at 36–42 dpf, foxl2a expression was higher at 24–30 dpf and significantly higher than that in males at 36–45 dpf. At 27 dpf, the meiosis-related genes dmc1 and sycp3 were detected, with expression patterns aligning with germ cell development and sex differentiation. In conclusion, by characterizing germ cell morphology and analysing expression changes in sex-related genes, we confirmed that sex determination in mandarin fish occurs before 27 dpf. In females, sex differentiation progresses from 27 to 51 dpf, whereas in males, it occurs from 33 to 57 dpf.

To better understand how gene transcription is controlled under different physiological and environmental conditions, we assessed transcription and methylation responses in a vertebrate system (salmon) where growth can be manipulated in response to growth hormone transgenesis or under satiated, feed-deprived, and re-fed experimental conditions. In both transgenic and non-transgenic liver tissue, methylation of gene promoters was negatively associated with transcription at all measured times. However, the changes in promoter methylation among time-points did not generally correlate with changes in gene transcription among treatments. The results from this study suggest that only a subset of genes are readily responsive to changes in promoter methylation for a given environmental shift such as feed-deprivation or a physiological shift such as growth hormone transgenesis (i.e., genotype-by-environment interactions). The present study also reveals the complexity of how one tissue responds to alterations in internal changes in physiology (growth modification by growth hormone transgenesis; genotype), external environmental conditions (food availability; environment), and their interactions (genotype-by-environment effects).

Poly(3-hydroxybutyrate), P(3HB), is an aliphatic polyester that is susceptible to biodegradation even in marine environments. The high biodegradability of P(3HB) can be attributed to the presence in the environment of extracellular P(3HB) depolymerase (PhaZ), the initial enzyme involved in P(3HB) degradation. In this study, we aimed to identify the gene encoding PhaZ in the marine P(3HB)-degrading bacterium Alteromonas sp. D210916BOD_24, which was previously isolated. First, we conducted genome analysis of the strain, revealing that the strain possesses a PhaZ homolog. It possesses a catalytic domain with a lipase box near the center, a substrate-binding domain comprising two regions, and a fibronectin type III linker domain, which fit the marine bacterial domain pattern. Disruption of the PhaZ homolog gene caused the strain to lose its P(3HB) degradation ability. The recombinant PhaZ homolog protein exhibited significant activity toward P(3HB). The results indicated that the PhaZ homolog indeed functions as PhaZ in Alteromonas sp. D210916BOD_24. Furthermore, we focused on the distribution and genomic placement of PhaZ homolog genes. The PhaZ homolog was present in 4/20 Alteromonas strains examined, with Alteromonas sp. D210916BOD_24 showing substantial divergence from the other three strains in the 16S rDNA-based phylogenetic tree. The gene arrangement around the PhaZ homolog gene was clearly different between Alteromonas sp. D210916BOD_24 and the others. Additionally, large-scale gene locations and orientations exhibited considerable differences. These findings suggest that the horizontal transfer of PhaZ homolog genes occurred after a certain degree of species division.

Despite being evolutionarily and commercially important, molluscs have been a traditionally challenging group to study, due to their difficulty in maintenance under lab conditions and the lack of a genetic toolkit. Previously, we showed that transgene expression can be attained in molluscan cells with reporter genes under a molluscan virus promoter sequence. Following up, we developed a simple, efficient and rapid transgene expression platform using primary hemocyte culture of Farrer’s scallop Chlamys farreri, a marine bivalve mollusc. The protocol consists of two steps: collection and seeding of hemocytes and incubation for 1 to 4 days with DNA-reagent mixture. We evaluated seven transfection reagents for three bivalve species and found that X-tremeGENE 360 was highly efficient for DNA transfection, particularly for C. farreri. Subsequently, C. farreri hemocyte culture and transfection conditions were examined, such as culture medium, size and form of DNA, and the mixing ratio of DNA and transfection reagent. Using this protocol, we visualized the subcellular localization of four bivalve oncogenes, Cf-Mdm2-like, Cf-c-Myc-like, Cf-Mortalin-like, and Cf-Ras-like, tagged with EGFP. Our hemocyte platform provides an easy entry to study cellular and molecular biology of molluscs and can be readily adapted for advanced methods such as live imaging and DNA–protein interaction assays, making the study of molluscs more accessible to the scientific community.

Unlike mammals with determinate growth patterns, large-bodied teleost fish exhibit indeterminate growth. Two distinct muscle stem cell populations have been discovered in teleost fish: muscle satellite cells expressing Pax3 and Pax7, akin to those in mammals, and growth-specific stem cells in the external cell layer (ECL) regulated by Meox1. However, their origins and regulatory mechanisms remain elusive in large teleost fishes. In this study, we identified these two stem cell populations in the golden pompano (Trachinotus ovatus), an economically significant teleost species. In situ hybridization revealed that muscle satellite cells are localized in mononucleated cells at the edges of muscle fibers, while growth-specific stem cells are distributed within the myosepta. Interestingly, growth-specific stem cells in T. ovatus differ from those in zebrafish in their origin, distribution, and expression patterns, which could be a contributing factor to T. ovatus’s ability for indeterminate growth, whereas zebrafish exhibit determinate growth. Investigations into the repair and regeneration of skeletal muscle following injury demonstrated that Meox1 also plays a role in repairing injured skeletal muscle, although its involvement occurs later than that of Pax3a/Pax7a. In conclusion, our findings confirm the presence of two distinct muscle stem cell populations in teleost fish, shedding light on the complexity of muscle growth. This research provides insights into muscle development and regeneration, with potential applications in aquaculture for improving muscle growth in economically important fish species.