Marine Biotechnology最新文献

China harbors extensive saline-alkaline water resources with considerable potential for aquaculture development. However, their utilization is constrained by high pH, elevated carbonate alkalinity, and complex ionic composition. Exopalaemon carinicauda, a commercially important shrimp species in China, is recognized for its environmental adaptability, rapid growth, desirable flesh quality, and high economic value. Owing to its resilience to diverse environments, E. carinicauda serves as an ideal model for investigating the molecular mechanisms underlying saline-alkaline adaptation in crustaceans. Yet, the genetic determinants of its alkalinity tolerance remain poorly understood, hindering selective breeding efforts. In this study, bulked segregant analysis (BSA) coupled with next-generation sequencing was employed to identify single nucleotide polymorphisms (SNPs) associated with alkalinity tolerance. DNA from individuals exhibiting extreme phenotypes was pooled, and allelic differences were assessed using Euclidean distance, deep learning, and ΔSNP-index methods. A total of 20,879,626 SNPs were detected, and seven candidate genomic regions spanning 47.53 Mb on chromosomes 4, 11, 13, 18, 26, and 36 were identified, encompassing 194 genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed significant associations with GABAergic synapse, taste transduction, and vasopressin-regulated water reabsorption. Comparative transcriptomic analysis under high-alkalinity stress in hepatopancreas and gills identified 28 genes strongly linked to alkalinity tolerance, including gamma-aminobutyric acid receptor, glutamate receptor ionotropic, and basic salivary proline-rich protein. Two SNP loci, C4-2601 and C8-6550, significantly associated with alkalinity tolerance were validated through PCR-based sequencing. These findings provide critical insights into the genetic architecture of alkalinity tolerance in E. carinicauda, facilitating future genomic and marker-assisted selection strategies.

The black rockfish (Sebastes schlegelii), an economically important ovoviviparous teleost in Chinese aquaculture, exhibits a distinctive reproductive strategy characterized by internal fertilization and prolonged embryonic development within females until live birth. However, this reproductive mode poses substantial challenges in artificial breeding practices due to a poor understanding of pregnancy (hereafter referring to intraovarian gestation in S. schlegelii) maintenance mechanisms. Here, we conducted a comparative genomic analysis between S. schlegelii and representative oviparous and ovoviviparous fishes, identifying 374 lineage-specific gene families associated with cellular signaling, metabolic regulation, immune response, and developmental processes. In addition, 73 gene families with significant expansions were identified to be mainly involved in extracellular matrix (ECM) structure and regulation, and neuromodulation. Furthermore, 164 genes potentially associated with mitochondrial function, metabolic pathways and angiogenesis were subjected to strong positive selection. Notably, expression profiles of candidate functional genes associated with ECM structure and regulation, and angiogenesis were detected using transcriptomic data of stage V ovary, optic vesicle stage, and pigmentation stage for ovarian stroma tissue, highlighting the vital roles of ECM remodeling and angiogenesis during pregnancy. These findings provide novel insights into the molecular mechanisms underlying pregnancy maintenance in S. schlegelii and contribute to a broader understanding of the genetic adaptations with pregnancy in ovoviviparous teleosts.

Mollusks are an abundant group of animals, with many ecologically and economically important members that are phylogenetically distinct from nearly all genetic model organisms. This study provides a clade-wide evaluation of small RNA biogenesis pathways, with emphasis on the eastern oyster, Crassostrea virginica. A more thorough characterization of these molecules supports rationale design of RNA interference (RNAi) approaches for manipulation of mollusk genetics. Like other animal groups, mollusks have conserved microRNAs (miRNAs), with some shared with ecdysozoans and deuterostomes; however, there was no evidence of a dedicated endogenous small-interfering RNA (siRNA) pathway. These findings suggest that alternatives to long double-stranded RNA (dsRNA)-mediated knockdown, specifically short-hairpin RNAs or small duplex RNAs, are likely more appropriate for gene silencing in mollusks. The study also finds abundant Piwi-interacting RNAs (piRNAs) in both soma and gonads with some mollusk-specific aspects. Many invertebrates exhibit somatic piRNAs; however, mollusk piRNAs appear to be restricted to a subset of cells, suggesting that the potential of piRNA-based RNAi is also limited. Further, individual animals also express a unique collection of piRNAs that seem to be only partially determined through inheritance from parents. Together, this work defines the RNAi mechanisms in mollusks and provides insights into the phenotypic diversity seen in this group.

Using vacant saline-alkali land for aquaculture has the advantages of resource utilization and significant economic and ecological benefits, but there is a need to understand the impact of variable alkalinity on aquacultural species. This study investigated the impact of different alkaline stress conditions (10 and 20 mmol/L) on transcription and changes in intestinal microbial communities in the oriental river prawn, Macrobrachium nipponense, over a 96-h period. Under low alkalinity conditions, pathways related to carbohydrate metabolism were activated, including glycolysis/gluconeogenesis, mannose metabolism, ascorbate and aldarate metabolism, carbohydrate binding, chitinase activity, and lysosome. Such conditions also led to an increase in the number of beneficial intestinal bacteria, such as Proteobacteria, Firmicutes, Actinobacteriota, and Acidobacteriota. However, high-alkaline conditions inhibited the fibroblast growth factor receptor signaling pathway, store-operated calcium channel activity, and MAPK signaling pathway, and significantly increased the number of pathogenic intestinal bacteria, such as Citrobacter. These results suggest that low alkalinity would promote the growth of M. nipponense by activating the glycolysis pathway and increasing the number of beneficial bacteria. By contrast, high alkalinity would inhibit their immune performance by affecting key signal transduction pathways and increasing harmful bacteria in the intestinal tract. Such insights provide a theoretical basis for the subsequent adaptive aquaculture of M. nipponense in saline-alkali areas.

Sea cucumber Apostichopus japonicus is one of the key aquaculture species in China, possessing high nutritional and medicinal value. However, significant variations in growth are commonly observed among individuals during their development. This study investigates the differences in gut microbiota composition, digestive capacity, and metabolic pathways in A. japonicus, aiming to elucidate the underlying relations contributing to growth rate discrepancies from the perspective of gut microbiota. Intestinal tissues were collected from individuals exhibiting marked growth differences, but Sharing the same genetic background And growth environment, for 16S rRNA sequencing analysis. Although no significant differences were observed in alpha diversity at the ASV level, differences in phylum level proportions suggest potential functional variations. We found significant differences in the gut microbiota between fast-growing and slow-growing A. japonicus by LEfSe analysis. The abundance of fast-growing individuals in Verrucomicrobiota, Verrucomicrobiaceae, and Haloferula was significantly increased. Additionally, significant differences in the enrichment of gut microbiota metabolic pathways were observed; the fast-growing group demonstrated higher overall metabolic activity, and body weight showed a significant positive correlation with glyoxylate and dicarboxylate metabolism and purine metabolism. The digestive capacity of fast-growing A. japonicus was significantly enhanced. Furthermore, fast-growing individuals exhibit a more complex metabolic network involving various biomolecular synthesis and metabolic pathways. These findings suggest that the differences in the growth rate of A. japonicus are primarily related to the functional activity of the gut microbiota; in particular, the improvement of digestive capacity and the activation of specific metabolic pathways may play a key role in promoting the growth of the host. Understanding these microbial influences provides valuable insights into the biological mechanisms underlying growth variation and may contribute to the development of strategies for optimizing sea cucumber aquaculture.

Fish epithelial surfaces are covered by a mucus layer. The highly glycosylated proteins called mucins are a main component of the mucus, which also contains a range of antibacterial enzymes, proteins, and peptides of importance for its protective properties. Here, we compared the practicality and yield of mucus harvesting from barramundi and Atlantic salmon epithelial sites using glass slide, swab, Super·SAL™ and whole tissue extract. We also compared the feasibility of using the orcinol assay, a glycan-on-membrane assay, and absorbance at 230 nm in combination with standard curves of pig gastric mucin to estimate the mucin concentration. Glycomics demonstrated that non-amine hexose content differed more between fish and tissues than terminal monosaccharides with cis-hydroxy groups, and that non-mucin molecules had a major impact on the A230-based results, making the glycan-on-membrane assay the most versatile method for estimating mucin concentration. We conclude that the most versatile tool for mucus harvesting was swabs, allowing for sufficient amounts of sample to be harvested with relative ease and low levels of contamination from the oral cavity, gill, skin, and intestine. Furthermore, the glycan-on-membrane assay was useful for measuring mucus concentration, and it was beneficial to estimate both sample concentration and purity by comparing samples at relatively similar concentrations.

In this study, Lactobacillus plantarum, Bacillus subtilis, and their 1:1 mixture were introduced into the aquaculture system of Micropterus salmoides for a duration of 42 days. Subsequently, a challenge test with Aeromonas hydrophila was performed. The objective was to evaluate the immunomodulatory and microbiota-regulating effects of these probiotics, with emphasis on intestinal microbial composition and serum metabolome shifts in treated versus control groups before and after infection. Results revealed a significant reduction in the relative abundance of A. hydrophila in the intestines of probiotic-treated fish (p < 0.05). Histological observations indicated improved intestinal integrity in treated groups. Metabolomic analysis identified significant alterations in serum compounds, particularly in carboxylic acids, organic oxygen compounds, glycerophospholipids, and fatty acyl derivatives (p < 0.05). Post-challenge, levels of pro-inflammatory metabolites were significantly lower in probiotic groups compared to controls. Microbial network analysis showed increased community modularity and stability in treated fish, with key shifts toward dominant genera such as Plesiomonas. These findings demonstrate that L. plantarum and B. subtilis effectively modulate host gut microbiota, reshape systemic metabolite profiles, and enhance immune resilience against bacterial infection. The observed microbiota–metabolome interactions underline the potential of these probiotics as functional feed additives for promoting fish health. The study provides mechanistic insights supporting the broader application of probiotic interventions in aquaculture and functional food development.

Siniperca scherzeri is an important aquaculture species in China with good disease resistance, but its growth rate is relatively slow. To uncover the molecular mechanisms underlying growth trait differences, this study employed RNA-seq technology to analyze the liver tissues of fast-growing (FG) and slow-growing (SG) individuals of S. scherzeri. A total of 875 differentially expressed genes (DEGs) and 622 differentially alternatively spliced genes (DSGs) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs were mainly involved in skeletal development, extracellular matrix remodeling, signal transduction, and cell growth and apoptosis, whereas the DSGs were significantly enriched in processes such as RNA splicing and processing, protein degradation, ribosome biogenesis, muscle structure and contraction, and were associated with multiple energy metabolism and signaling pathways. Alternative splicing analysis revealed that, compared with the slow-growth group, the fast-growth group exhibited a higher abundance of alternative splicing events. These results suggest that the growth differences in S. scherzeri may stem from the coordinated regulation at both the transcriptional and splicing levels, thereby contributing to enhanced growth rates. These findings provide important insights into the molecular basis underlying growth differences in S. scherzeri and offer valuable resources for the identification of potential molecular markers and key functional genes for aquaculture breeding.

Epinephelus tukula is an economically important aquaculture animal, and a major parent in grouper crossbreeding. To better preserve and exploit E. tukula germplasm resources, a core collection (containing 34 individuals derived from 10 genetic groups) was first constructed based on phenotypic growth traits and whole-genome resequencing (WGS) data. The phenotypic traits of the individuals within the core collection were not significantly different from those in the original collection, suggesting effective representativeness of the core collection. Additionally, we performed genome-wide association study (GWAS) of E. tukula to identify candidate single nucleotide polymorphisms (SNPs) and genes associated with growth traits, to facilitate the improvements in the growth performance of this species. Twenty-six significant SNPs were identified, scattered among multiple chromosomes. Five SNPs were confirmed to be correlated with growth in another new group of 101 individuals. Based on the annotation results, these five SNPs were located in CCDC102A, NTRK2, CTSL, OTOF, and nestin, and were involved in cell development, differentiation and proliferation, glycolytic metabolism, neurological development, and myoblast differentiation. Our findings not only provide an effective basis for the conservation and utilization of E. tukula germplasm resources, but also promote the development of marker-assisted selection of E. tukula.