Marine Biotechnology最新文献

Copper ion pollution poses a significant threat to marine ecosystems. Seaweeds exhibit potential for metal bioremediation through their inherent mechanisms of metal absorption and tolerance. However, the understanding of seaweed resistance to metal ions, particularly copper, continues to evolve, despite previous studies elucidating some underlying molecular mechanisms. This study delineates the transcriptomic adaptations of Oocystis borgei to copper exposure via RNA-seq, highlighting its remarkable bioremoval efficacy, consistently averages 82%. RNA sequencing revealed profound alterations in transcriptomic profiles, which were further examined through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyses. This comprehensive examination identified key mechanisms facilitating copper absorption and enhanced tolerance in Oocystis borgei, including transporter activity, oxidation-reduction processes, photosynthesis, and glutathione metabolism. Overall, this analysis provides essential insights into the molecular mechanisms driving seaweed adaptive responses to copper-induced stress, laying the groundwork for future studies on their bioremediative capabilities.

Graphical Abstract

Perkinsus olseni is a highly pathogenic protozoan parasite affecting mollusks worldwide, posing a significant threat to Manila clam (Ruditapes philippinarum) aquaculture. This study investigated the impact of natural P. olseni infection abundance on the gill lipid metabolism of clams collected from Dandong City, Liaoning Province. The parasite species was identified via Polymerase Chain Reaction (PCR), while infection prevalence, abundance, and infection grade classification were assessed using Ray’s Fluid Thioglycolate Medium (RFTM) culture. Lipid metabolomics analysis was performed to compare lipid profiles among uninfected (Neg), lightly infected (L), and moderately infected (M) clam gills. Results confirmed the presence of P. olseni with an overall prevalence of 91%. The infection abundance was significantly higher in the gills and digestive gland than in the mantle and siphon tissues. Lipidomic analysis of 18 samples (6 biological replicates per Neg, L, and M group) using a Liquid Chromatography-Mass Spectrometry (LC-MS) platform identified 1,561 metabolites, with significant differences observed across infection groups. 28 differential lipid metabolites were common to both the L and M groups when compared to the Neg group. KEGG pathway enrichment and correlation network analysis highlighted two key metabolites: diacylglycerol (DG) (16:0/18:2) and triacylglycerol (TG) (18:0/18:1/18:2). These metabolites were associated with 13 pathways, including T cell receptor signaling, fat digestion and absorption, and regulation of lipolysis in adipocytes. These findings elucidate tissue-specific infection patterns and reveal lipid metabolic reprogramming in clam gills in response to P. olseni, providing insights into host-parasite interactions and potential metabolic biomarkers for perkinsosis.

The study investigated the effect of ultrasonic radiation on the growth of Chlorella microalgae cells and the accumulation of intracellular metabolites (intracellular water-soluble proteins, lipids) in them. The results of the study showed that daily ultrasonic radiation (72 J/ml) with a power of 300 W for 60 s had a significant positive effect on the growth rate of microalgae. Increasing the ultrasound power from 20 W (4.8 J/mL) to 300 W (72 J/mL) resulted in a 1.3-fold increase in cell concentration in suspension and 1.4-fold increase in biomass concentration after 24 days of cultivation. The positive effect of ultrasound treatment on the process of periodic cultivation of microalgae is attributed to the acceleration of metabolism due to the increase in temperature of the suspension and the destruction of extracellular phenolic metabolites that inhibit the nitrate-anion transport system. In addition, ultrasound has a positive effect on the accumulation of intracellular metabolites in the biomass (the concentration of intracellular water-soluble proteins and total lipids became 1.4-fold and 2-fold higher, respectively, compared to the control). The research aims to increase the efficiency of the cultivation stage and may have practical significance for microalgae producers and researchers involved in the development of new methods to improve the production and obtain valuable substances from microalgae.

The sulfated polysaccharides derived from marine species have attracted attention for their nutraceutical and pharmaceutical potential. Initially examined in cell culture, many labs have further tested their activity in in vivo rodent assays. Zebrafish embryos have been recently proposed as an alternative model species to test anti-inflammatory, fungicidal, immunomodulatory, antioxidant, antitumour, or toxicity effects with significant success. In this article, we systematically review by PRISMA strategy the assays that use zebrafish to evaluate potential nutraceutical and pharmaceutical applications of polysaccharides from more than 30 marine algal species. Effects against cancer, inflammation, and oxidative stress or over regeneration capacity, immunomodulation, and photoprotection in zebrafish are here compared. From this review, some polysaccharides appear as safe antitumour compounds (e.g. neutral S. skottsbergii–derived fraction over G-361 melanoma) while others show significant toxicity to embryos. The current bibliography shows a clear trend to use in parallel zebrafish larvae and in vitro assays to test the effects of polysaccharide fractions recovered from a variety of bioprocesses from different marine algae–derived biomass. Its potential application in the pharmacology and nutraceutical industry is discussed.

Mollusk shell formation is a delicate and comprehensive physiological process that relies on the precise deposition of crystals under the control of shell matrix proteins. However, the underlying protective mechanisms governing this process remain largely unknown. Herein, a novel shell matrix protein gene was identified from the freshwater mussel, Hyriopsis cumingii. The predicted protein is characterized by a high glycine content and two Kunitz-type SPI domains, designated as HcGrKuSPI. The HcGrKuSPI gene was highly expressed in the outer epithelial of the mantle edge and mantle pallial. Immunostaining in situ analysis revealed the presence of HcGrKuSPI in the thick inter-prism matrix of the prismatic layer and the organic membrane of the nacreous layer. The expression of HcGrKuSPI in the pearl sac significantly increased during the ordered deposition of pearl nacre tablets. The resultant recombinant protein, SUMO-HcGrKuSPI, exhibited a strong affinity for aragonite and calcite and was involved in the morphological modification of calcite crystals in vitro. These results indicate that HcGrKuSPI is involved in organic framework construction and crystal morphological modification during the prismatic and nacreous layers formation. Furthermore, the expression of HcGrKuSPI in the mantle significantly increased following bacterial infection within the extrapallial fluid, and SUMO-HcGrKuSPI exhibited a strong inhibitory effect against bacterial growth and trypsin activity. Antibody injection in vivo led to severe damage to the thick inter-column framework of the prismatic layer and morphological deformities of nacre tablets. These findings indicate that HcGrKuSPI exhibits excellent protease inhibitory and antibacterial activities, providing a matrix protection system to ensure the smoothness of shell and pearl formation. Overall, these results enhance our understanding of the protective mechanisms involved in mollusk biomineralization.

Genome research has dominated life sciences research in the last two decades. Of approximately 11,000 sequenced vertebrate genomes, genomes of teleost fish represent about 30%, with reference genome sequences available for most aquaculture fish species. While such progress has accelerated progress in aquaculture genetics research and breeding, it is clear that understanding of full genomic variations among aquaculture species is lacking. This is largely because of the way reference genomic sequences were produced, with a single or just a few genomes being sequenced. In addition, haplotype variations and their representation in the species or population are unknown. This hinders understanding of genomic basis of phenotypic variations relevant to performance and production traits such as growth rates, feed conversion efficiency, disease resistance, stress responses, processing yields, and reproductive traits, among other traits, especially so with strain-specific performance traits. The pangenome refers to a whole collection of genomic sequences found in the entire species or population rather than in a single individual, as represented in reference genomes. Pangenome includes the core genome sequence that are shared in all individuals, and variable or dispensable genome sequence found in a subset of individuals, representing intraspecies genomic variations. In this review, we present the current state of reference genomes and reference pangenomes, compare the advantages and disadvantages of various methods in producing pangenomes, propose the concept of pangenome plus (pangenome⁺) to include genomes of related species with which interspecific hybrids can be made to introgress the beneficial genes. Revealing full genomic variations, determination of genomic variations relevant to performance traits, and combining beneficial genes and alleles into aquaculture breeds are three most important steps for the application of genome-based technologies to aquaculture breeding. To accomplish these three steps is challenging but offers unprecedented opportunities for aquaculture.

Developing effective molecular indicators to monitor stress status of coastal species is a top priority due to the impacts of climate change. However, the complexity of stress responses, which are regulated by multiple genes, limits the effectiveness of single-gene approaches in accurately reflecting stress status. Transcription factors (TFs) are promising candidates for comprehensively assessing stress responses, as they regulate numerous stress-responsive genes. In this study, we present a framework for identifying TF indicators that reflect the stress status of Pacific oysters (Crassostrea gigas). Specifically, oysters were exposed to high, medium, and low tide conditions to assess the physiological responses of oysters to tidal-induced stress. Enrichment analysis of differentially accessible chromatin peaks derived from assay for transposase-accessible chromatin sequencing (ATAC-seq) identified several key TFs. Among these, CCCTC-binding factor (Cg-CTCF) and MYB proto-oncogene A (Cg-MYBA) were significantly upregulated under tidal-induced stress and occupied critical positions in regulatory networks, as indicated by RNA-seq. RNA interference experiments confirmed that both genes contribute to enhancing survival under heat stress, a major stressor affecting oysters. Additionally, field experiments demonstrated significant upregulation of these genes under natural stress conditions, suggesting their potential as indicators for oyster reef management. To our knowledge, this is the first study on the coastal invertebrate to combine ATAC/RNA-seq with in vivo TF knockdown and field validation to propose TFs as practical stress indicators. We advocate for the broad application of our framework to explore TFs as molecular indicators of health status in marine organisms, thereby enabling informed strategies for conservation management.

In DUI animals, two sex-specific mitochondrial lineages are present: one transmitted maternally (F-type) and the other paternally (M-type), each containing a sex-specific mitochondrial ORFan gene. Comprehensive in silico characterization of DUI ORFan proteins has been conducted in freshwater mussels, with partial studies in marine mussels; however, research in other DUI species remains scarce. In this regard, we newly identified two DUI species, Antigona lamellaris (Schumacher, 1817) and Ezocallista brevisiphonata (P. P. Carpenter, 1864), and analyzed the major unassigned regions of the mitochondrial genomes in 169 specimens from eight species of Veneridae, verifying the presence of novel mitochondrial ORFs. Structural and functional analyses were performed on 14 ORFans, and the conservation patterns and properties of DUI ORFans in Veneridae were further explored by integrating in silico characterization results from freshwater and marine mussels. Strong structural and functional similarities were found between F-ORF and M-ORF proteins, both across different bivalve species and within the studied species. In contrast to freshwater and marine mussels, the F and M-ORF sequences in Veneridae show remarkable similarity. Additionally, apart from sex-specific ORFs, reverse ORFs (ORFs encoded on the reverse strand) were identified in Antigona lamellaris. Predicted transmembrane (TMs) number and topology analysis suggest that ORFs in Veneridae exhibit lower conservation compared to those in freshwater mussels. Our findings support the hypothesis that ORFans may originate from viruses or from proteins involved in mitochondrial energy production, providing further evidence for the multiple origins of ORFs. We propose that Veneridae, freshwater mussels, and marine mussels may harbor DUI systems with distinct origins and modes of action. The connection between ORFan proteins and DUI systems may differ across these taxa.