Marine Biotechnology

Zhang, Yifei; Li, Qi

doi: 10.1007/s10126-026-10669-4pmid: 42399438

Carotenoids are widely regarded as the main pigments driving yellow to orange shell coloration in mollusks, yet their role remains poorly understood in the economically important Pacific oyster Crassostrea gigas with abundant shell color morphs. To fill this research gap, we integrated Raman spectroscopy, HPLC detection, dietary supplementation trials, and gene expression profiling across four selectively bred strains with black (SB), white (SW), gold (SG), and orange shells (SO). Raman spectra revealed distinct pigment compositional profiles among different shell color morphs but displayed no characteristic carotenoid peaks within the 1500–1550 and 1150–1170 cm⁻¹ wavenumber ranges. Although HPLC detected only trace amounts of fucoxanthin in golden shells, carotenoid concentrations in the mantle showed no correlation with shell color and fluctuated markedly under different environmental conditions. Furthermore, a 28-day dietary supplementation trial verified that carotenoids were neither incorporated into shell structures nor did they contribute to mantle pigment deposition. Notably, key genes involved in carotenoid metabolism, including CgAPO, CgBCO, and CgSR-BI, were significantly upregulated in the hepatopancreas after dietary carotenoid feeding but were not expressed in mantle tissues, implying their physiological role in metabolic utilization rather than pigment allocation for shell coloration. Collectively, these findings challenge the conventional view that carotenoids dominate molluscan shell pigmentation, demonstrating that C. gigas deviates from the canonical carotenoid-based coloration paradigm, offering valuable insights for the genetic improvement of oyster color traits and advancing our understanding of molluscan pigmentation.

Sung, Tzu–Yuan; Shih, Pei-Chi; Chen, Bonien; Hong, Ming–Chang

doi: 10.1007/s10126-026-10661-ypmid: N/A

Extracellular vesicles and EV-enriched extracellular particles are increasingly recognized as potential mediators of intercellular communication. In coral reef ecosystems, dinoflagellate symbionts of the family Symbiodiniaceae play central roles in host metabolism, environmental acclimation, and stress responses; however, the molecular composition of extracellular particles released by cultured Symbiodiniaceae remains poorly understood. In this study, a host-isolated Symbiodiniaceae culture derived from the sea anemone Exaiptasia diaphana was established under host-free laboratory conditions for EV-enriched particle isolation and characterization. Physicochemical analysis of the recovered extracellular particle fraction showed an average diameter of 534.1 ± 63.9 nm, a polydispersity index of 0.733 ± 0.08, and an average zeta potential of − 14.57 ± 1.55 mV, indicating a heterogeneous and negatively charged extracellular particle suspension. Small RNA analysis showed that the EV-associated RNA fraction contained multiple RNA biotypes, with rRNA- and tRNA-derived reads representing the dominant annotated components, whereas miRNA-like sequences accounted for only a minor fraction of the annotated small RNA pool. Comparison against an antisense Exaiptasia diaphana CDS dataset further identified retained EV-associated small RNAs showing sequence complementarity to host coding transcripts, including cytohesin-1 and EPG5. These matches are interpreted as candidate sequence-level observations rather than evidence of functional host regulation. In parallel, miRNA-oriented analysis identified candidate miRNA-like sequences after downstream filtering. Proteomic profiling by LC–MS/MS generated 4,086 accession-level matches. After removal of uninformative entries and consolidation of duplicate protein names, 834 non-redundant named proteins were retained and classified into nine functional groups, including proteins involved in metabolism and energy production, transport and membrane trafficking, photosynthesis and chloroplast function, and signal transduction and regulation. Representative annotations included 14-3-3-related proteins, Rab/ARF family proteins, Hsp70, Hsp90, and oxygen-evolving enhancer protein. These results provide an initial qualitative molecular characterization of EV-associated molecules released by a host-isolated Symbiodiniaceae culture and serve as a baseline for future studies of algal extracellular communication and cnidarian–dinoflagellate symbiosis.

Abd Rahim, Noorul Darlina Edlin; Waiho, Khor; Tan, Min Pau; Sung, Yeong Yik; Altaf-Ul-Amin, Md.; Kanaya, Shigehiko; Mohamed-Hussein, Zeti-Azura; Afiqah-Aleng, Nor

doi: 10.1007/s10126-026-10655-wpmid: N/A

Whiteleg shrimp, Penaeus vannamei, is the most cultured shrimp species worldwide and plays an important role in global aquaculture production, food security, and economic growth. Nonetheless, infectious diseases, including acute hepatopancreatic necrosis disease (AHPND), can severely threaten the sustainability of shrimp production. These impacts may also be exacerbated by climate-related environmental stressors, such as temperature and salinity, which further disrupt host metabolism and immunity. Although many shrimp genes have been reported in AHPND studies, the molecular interactions underlying host responses to this disease remain unclear. Therefore, this study aims to investigate the potential molecular mechanisms of AHPND by identifying sets of interacting proteins and associated biological functions using network clustering. The P. vannamei AHPND-related proteins (PvAHPNDrp) were identified via bibliomic analysis and used to construct the AHPND protein-protein interaction (PPI) network. The network was clustered using the DPClusO algorithm, and statistically enriched clusters were identified using the PvAHPNDrp distribution. Functional enrichment analysis was subsequently performed to determine the potential biological functions associated with AHPND mechanisms. The analysis identified significant clusters with interactions of PvAHPNDrp and non-PvAHPNDrp, including glutamine-, proline-, and tyrosine-tRNA ligases, and alpha-1,4-N-acetylglucosaminyltransferase. Enriched biological functions, such as aminoacyl-tRNA ligase activity and lipid metabolic process, may be associated with P. vannamei’s response to AHPND. Collectively, this study provides a systems-level perspective on the molecular interaction networks associated with AHPND and identifies candidate proteins and functions for future experimental validation, contributing to improved understanding of disease mechanisms and supporting climate-resilient shrimp health management strategies.

Li, Sixun; Wu, Mengmeng; Zhang, Min; Xie, Zihang; Lai, Jie; Zhan, Lilin; Deng, Ziyan; Cai, Guojun; Gong, Jian; Han, Chong; Li, Qiang

doi: 10.1007/s10126-026-10662-xpmid: 42397635

Xu, Xiaoyan; Du, Meirong; Jiang, Zengjie; Lyu, Jianfu; Jiang, Weiwei; Zhang, Jinghan; Sun, Chao; Zhang, Yitao; Wang, Junwei

doi: 10.1007/s10126-026-10634-1pmid: N/A

Many marine invertebrate larvae are influenced by environmental factors during development, with diatom biofilms playing a crucial role in the settlement and metamorphosis of bivalve larvae. This study found that Navicula sp. biofilms alter the larval microenvironment by increasing dissolved oxygen levels through photosynthesis and decreasing nitrate, ammonium, and phosphate levels in the surrounding water. Exposure to Navicula sp. biofilms induced directional swimming in larvae and significantly shortened the time required for settlement and metamorphosis. Biofilms formed by Navicula sp. contained effective substances and key infochemicals that promoted the settlement and metamorphosis of Mizuhopecten yessoensis larvae. Soluble polysaccharides containing β-1,4-glycosidic bonds secreted by the biofilm were recognized by the larvae, triggering settlement and metamorphosis signaling. Untargeted and targeted metabolomic analyses revealed increased levels of cGMP (Cyclic guanosine monophosphate), and GMP (Guanosine monophosphate), suggesting that larval settlement and metamorphosis may be associated with cGMP regulation. Based on these results, cGMP was selected for subsequent functional analyses. Treatments with the NO donor SNAP, the cGMP analog 8-Br-cGMP, and the sGC activator BAY 41-2272 significantly promoted metamorphosis, whereas the sGC inhibitor ODQ suppressed metamorphosis in a dose-dependent manner. These findings demonstrate that the NO–sGC–cGMP pathway positively regulates the settlement and metamorphosis of M. yessoensis larvae, with cGMP serving as a key effector. This study provides new insights into the mechanisms underlying larval settlement and metamorphosis in bivalves.

Quintanilla-Mena, Mercedes; Góngora-Castillo, Elsa B.; Rodriguez-Canul, Rossanna; Rivera-Bustamante, Rafael

doi: 10.1007/s10126-026-10665-8pmid: 42377573

The lined sole, Achirus lineatus, is a widely distributed species in the Gulf of Mexico. This basin is constantly exposed to hydrocarbon contamination due to natural oil seeps, oil extraction and oil spills. Previous studies suggest the line sole A. lineatus as a possible sentinel species for oil spills; but the overall landscape of xenobiotic metabolism in this species remains poorly understood. Access to high-quality reference genomes will improve this situation. Here, we report the first whole-genome sequence, assembly, and annotation of the lined sole A. lineatus. We generated 132 Gb of PacBio High-Fidelity (HiFi) reads, which were filtered to retain 93 Gb of ultra-high-quality data. The assembly resulted in a mitogenome of 16,579 bp and a nuclear genome of 486.3 Mb distributed across 199 contigs, with a contig N50 of 9.87 Mb. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis based on the actinopterygii_odb10 database (3,640 orthologs) identified 3,611 (99.2%) complete BUSCOs. Genome annotation strategy resulted in the identification of 22,412 protein-coding genes with a high percentage (95.94%) of functional annotation. The genome of A. lineatus revealed 693 expanded and 3349 contracted gene families. We also identified 123 genes involved in the xenobiotics biodegradation and metabolism pathways, as well as neuroplasticity-related genes that may be associated with responses to environmental toxicants, providing baseline genomic information that suggests an integrated adaptive strategy involving both metabolic and nervous system processes. This assembly represents a valuable genomic resource for future toxicological and ecological studies of this species.

Yang, Qi; Wang, Shentong; Wang, Wei; Zhang, Guofan; Li, Li

doi: 10.1007/s10126-026-10658-7pmid: N/A

Biomineralization in mollusks, a fundamental process in marine ecosystems, is highly sensitive to anthropogenic stressors. Exosome-secreted species-specific shell matrix proteins (SMPs) are essential in biomineralization adaptation but remain understudied. Estuaries are considered unfavorable for biomineralization compared to open coastal zones and serve as an ideal research location to explore the roles of exosome-secreted species-specific SMPs in biomineralization adaptation under future rapid environmental change. Here, combining proteomics of shell matrix and mantle-derived exosomes, the high-abundance species-specific SMPs Car-TPM (tropomyosin from estuarine oyster Crassostrea ariakensis) and Cgi-GIGA6 (gigasin-6 from coastal oyster Crassostrea gigas) were taken as representatives to decipher the roles of exosome-secreted species-specific SMPs in oyster biomineralization adaptation. Tissue expression profiles and in situ hybridization revealed that Car-TPM was highly expressed in the adductor muscle and mantle, while Cgi-GIGA6 predominated in the mantle. Post-injury experiments demonstrated that Car-TPM expression upregulated quickly at 6 h, and Cgi-GIGA6 continued to be down-regulated. Knockdown of Car-TPM suppressed shell repair, whereas silencing Cgi-GIGA6 enhanced it. In vitro assays revealed that Car-TPM significantly promoted calcium carbonate precipitation and aggregation of rhombohedral calcite crystals, whereas Cgi-GIGA6 suppressed crystallization and eroded the original flat edges. These findings indicate that Car-TPM is a positive regulator of biomineralization in C. ariakensis inhabiting harsh estuarine environments, while Cgi-GIGA6 exerts a negative regulatory effect to optimize energy allocation by restraining excessive biomineralization in C. gigas. This study reveals the essential role of species-specific SMPs secreted via exosomes in the biomineralization adaptation and adaptive potential of mollusks in future marine environments.Graphical Abstract[graphic not available: see fulltext]

Casuso, Antonio; Leal, Yeny; Gallardo-Escárate, Cristian; Valenzuela-Muñoz, Valentina

doi: 10.1007/s10126-026-10663-wpmid: 42399510

Vaccine-based approaches provide a sustainable method for controlling pathogens in aquaculture. Our team previously created the IPath® vaccine, a recombinant formulation with metal-chelating properties. This study aimed to evaluate the performance of IPath® in salmon vaccinated with the mandatory vaccines used commercially in Chile, and to assess their effects on the transcriptome profiles of Atlantic salmon challenged with Caligus rogercresseyi and co-infected with Piscirickettsia salmonis. Four experimental groups of Atlantic salmon were immunized: IPath®, BlueGuard® (B) + Alpha Ject LiVac® SRS® (L), B + L + IPath®, and PBS as a control. After accumulating 400 thermal units (ATUs), vaccinated salmon were exposed to a coinfection model involving 35 copepodids per fish for 25 days, followed by an intraperitoneal infection with P. salmonis (1 × 10^8) for 16 days, with mortality recorded daily. Head kidney tissue samples were collected for mRNA Illumina sequencing at 25 days post-infection (dpi) for sea lice and at 16 dpi for P. salmonis infections. IPath® and B + L + IPath® showed 73.7 and 69.8% reduction in sea lice burden, respectively. Furthermore, the IPath® vaccinated group showed a delay in salmon mortality following P. salmonis infection compared with the other experimental groups. During sea lice infection, the B + L + IPath® group upregulated key immune-related genes, such as cathelicidin, major histocompatibility complex class I, and interferon regulatory factor, indicating an innate and adaptive immune response. During P. salmonis co-infection, the B + L group downregulated immune-related transcripts, including metalloendopeptidase, interferon regulatory factor 7, and T-lymphocyte surface antigen Ly-9-like. Biological processes and pathways related to stress response were highly enriched in the B + L group. Notably, the IPath® and B + L + IPath® groups triggered gene regulation associated with iron balance, such as ferric chelate reductase 1, in response to both pathogens. A synergy between IPath® and commercial vaccines, especially in iron regulation and immune response, offers a new approach for integrated control of C. rogercresseyi and P. salmonis in salmon farming.

Cheng, Xiangbing; Chen, Ziyi; Li, Fangcheng; Liu, Qigen; Hu, Wenjing; Sun, Jiamin

doi: 10.1007/s10126-026-10666-7pmid: 42384105

Domestication has profoundly transformed human production and lifestyles. The Qingtian rice-fish co-culture system is the first globally important agricultural heritage system (GIAHS). PF-carp are a key species in the Qingtian rice-fish system and have been domesticated in rice paddies for more than a millennium, yet the mechanisms of their tolerance to high temperature conditions remain unresolved. In this study, 28℃ as the control group (C0), and two heat stress groups were established at 38℃ for 0 h (H0) and 24 h (H24). Brain tissues were sampled for physiological index measurements and transcriptomic analysis. Physiological analyses showed that the activities of SOD, CAT, and GSH-Px increased initially and then declined, whereas MDA levels exhibited a continuous increase. Transcriptome profiling identified 9,825 differentially expressed genes (DEGs). KEGG enrichment analysis of DEGs indicated that immune responses and metabolic regulation were consistently involved throughout the thermal adaptation process. During acute warming phase, pathways such as protein processing in the endoplasmic reticulum, FoxO signaling pathway and glycerophospholipid metabolism were enriched. Under prolonged high temperature exposure, cytokine-cytokine receptor interaction, PPAR signaling pathway and TGF-β signaling pathway were prominently enriched. Within these pathways, genes including grp94, hsp70, bip, nef, il-1r, tlr8, cctgα6, ccr4, cxcr3, and il-10 were significantly up-regulated (p < 0.05). These results indicate that PF-carp exhibit coordinated brain physiological and transcriptomic responses to high temperature exposure, involving protein quality control, immune signaling, and metabolic regulation. Collectively, our findings provide new insights into the mechanisms by which PF-carp adapt to thermal exposure and provide theoretical support for the breeding of heat tolerant fish.