Marine Life Science & Technology最新文献

Growth of the Pacific white shrimp Litopenaeus vannamei, the most important farmed crustacean, has consistently been a focal point for breeders. Over the past decades, some candidate genes for shrimp growth have been identified. However, further research is needed to elucidate the molecular regulatory mechanism of these genes. LvMmd2 was previously identified as a candidate gene that may inhibit the growth of L. vannamei. In this study, we analyzed the genotype and expression of the LvMmd2 gene in a breeding family and indicated its role as a growth-inhibiting gene. We found that LvMmd2 co-localized with its homolog LvPAQR3 at the Golgi apparatus. Using co-immunoprecipitation (Co-IP) and DUAL membrane system yeast two-hybrid (MbY2H), we indicated the interactions between LvMmd2 and LvPAQR3, LvPAQR3 and LvRaf1, as well as LvMmd2 and LvRho. These results suggest that LvMmd2 directly and indirectly regulates the Ras signaling pathway. Furthermore, we show that the LvMmd2 gene may indirectly affect the PI3K/AKT, insulin, and Hippo signaling pathways to regulate cell proliferation and differentiation via LvPAQR3 and LvRaf1. Through transcriptome and MbY2H analyses, we have also revealed the interaction between LvMmd2 and proteins involved in growth, immunity, protein transport, synthesis, and modification. These findings demonstrate the various molecular pathways through which LvMmd2 regulates L. vannamei growth. This study provides insights into the mechanism of shrimp growth regulated by Mmd2, enhances our understanding of LvMmd2 function, and highlights its potential application in shrimp breeding.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00273-7.

In this study, we investigated the molecular recognition mechanisms of shark-derived single-domain antibodies (ssdAbs) targeting fluoroquinolones using an integrated approach that combines in silico homologous modeling, molecular dynamics simulations, molecular docking, and alanine scanning mutagenesis. Three ssdAbs-2E6, 1N9, and 1O17-specific to enrofloxacin, norfloxacin, and ofloxacin, respectively, were selected based on previous work. Through AlphaFold2 and GalaxyWEB, the protein structures of these ssdAbs were predicted and optimized, followed by molecular dynamics simulations to emulate realistic protein behavior in a solvent environment. Molecular docking, alanine scanning mutagenesis, and subsequent verifications identified 30N and 93W of 2E6; 30N, 89R, 98Y, and 99D of 1N9; 100W and 101R of 1O17, all located within the complementarity determining region 3 loop, as critical for antigen binding. These residues primarily interact with their targets through hydrogen bonds, salt bridges, π-π stackings, and cation-π interactions. This study revealed, for the first time, the binding mechanism of ssdAbs to fluoroquinolones from a theoretical perspective, emphasizing the importance of aromatic and polar residues in recognizing characteristic epitopes, such as the carboxyl group at the C3 position and the 1-piperazinyl group at the C7 position. Our findings provide valuable insights for the rational design and enhancement of ssdAbs for detecting small molecule hazards in aquaculture.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00277-3.

Antarctic krill Euphausia superba, one of the most abundant species on the planet, is a keystone species of the Southern Ocean ecosystem. In the present study, we analyzed the RNA virome of Antarctic krill via metatranscription methods. The results showed that only 0.39% (49/12, 558) of the resultant unigenes could be assigned to known viral taxa, which were most similar to 17 known viruses, including nine invertebrate viruses, two vertebrate viruses, three protozoan viruses and three mycoviruses. However, most of the detected viruses possessed low amino acid similarity with counterparts in the viral databases. Penaeus vannamei picornavirus (PvPV; Family Picornaviridae) and covert mortality nodavirus (CMNV; Family Nodaviridae) were the two most abundant viruses in the Antarctic krill RNA virome. Notably, PvPV and CMNV are known pathogens to multiple aquatic animals according to epidemiological survey and exposure experiments, whereby PvPV positive krill caused clinical symptoms and histopathological lesions to P. vannamei and similarly, CMNV infection altered the swimming and feeding behavior of parent marine medaka Oryzias melastigma and caused tissue damage and even spinal curvature of the offspring. Results herein reveal, for the first time, the high abundance and taxonomic diversity of viruses in Antarctic krill while simultaneously highlighting the risk of an important virus reservoir to global aquaculture, and the potential impact on animals in the Antarctic ecosystem.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00270-w.

Declining populations and bottlenecks lead to the accumulation of deleterious mutations in fish populations. These processes also trigger genetic purging, which is a key genetic factor in reducing the deleterious burdens and increasing population viability. However, there is a lack of empirical evidence on the interaction between demographic history and the genome-wide pattern of deleterious variations. Here, we generated genome resequencing data of Eleutheronema rhadinum from China and Thailand, representing the major distribution of the species' southern regions. E. rhadinum had exceptionally low genome-wide variability and experienced dramatic population expansions followed by continuous declines. The geographical divergence, which occurred ~ 23,000 years ago, shaped different demographic trajectories and generated different regional patterns of deleterious mutations in China and Thailand populations. Several lines of evidence revealed that this geographical pattern of deleterious mutation was driven by the purging of highly deleterious mutations. We showed that purifying selection had inbreeding-associated fitness costs and was more efficient against missense mutations in the Thailand population, which had the lowest genetic burden of homozygous deleterious mutations. Multiple evolutionarily conserved protein domains were disrupted by the loss-of-function mutations, posing a high probability of gene functionality elimination. Moreover, thermal and salinity genes (Trpm3, Nek4, Gtf2f2, Cldn14) were identified in genomic divergence regions of E. rhadinum among China and Thailand populations. Our findings highlight the importance of demographic history factors shaping the geographical patterns of deleterious mutations. The results serve to deepen our understanding of the adaptive evolution and divergence of E. rhadinum with implications for other marine fish.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00276-4.

Nervous necrosis virus (NNV) is the etiological agent of viral encephalopathy and retinopathy in many fish species, including European sea bass (Dicentrachus labrax) and is of great economic losses to fish farmers. To solve this problem in fish production, antimicrobial peptides (AMPs) have been identified as potential candidates for NNV treatment in aquaculture. Hepcidin (Hamp) is one of the most promising AMPs. Thus, we aimed to evaluate the therapeutic application of Hamp synthetic peptide after NNV challenge. Hamp was able to significantly increase survival rates and ameliorate clinical signs of the disease, though the viral levels, determined by viral replication and immunolocalization, were not affected. Synthetic Hamp increased the immunoglobulin M (IgM) and AMP protein levels in serum and some tissues respect to the levels found in NNV-infected fish. However, Hamp peptide decreased the NNV-induced bactericidal activity. At the gene level, Hamp exerted anti-inflammatory properties, reducing the pro-inflammatory response orchestrated by NNV, probably preventing neuronal damage. Apart from this, Hamp up-regulated the expression of adhesion molecules that facilitated the recruitment of immune cells, namely T helper and B cells, probably to orchestrate the adaptive response. To conclude, Hamp immunomodulatory properties and therapeutic application against NNV are very promising for its use in aquaculture.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00262-w.

Free trans-4-hydroxy-L-proline (T4LHyp), a non-proteinogenic amino acid, is mainly released from the degradation of collagen, hydroxyproline-rich glycoproteins, and some peptide antibiotics in nature. Although it has been known that some terrestrial bacteria utilize T4LHyp as carbon and nitrogen source via a T4LHyp gene cluster, which and how marine microorganisms catabolize T4LHyp still remains unclear. Here, five T4LHyp-utilizing marine bacterial strains, Halomonas sp. 5021, Salinicola sp. 4072, Alteromonas sp. 6022, Alteromonas sp. 5112 and Alteromonas sp. 30521, were isolated from hydrothermal vent sediment samples collected from the southwest Indian Ocean. While Halomonas sp. 5021 can utilize T4LHyp as both a nitrogen and carbon source, the other four strains can utilize T4LHyp as only a nitrogen source. Then, the T4LHyp catabolic mechanisms of Halomonas sp. 5021 and Salinicola sp. 4072, as a representative of the four strains, were further investigated by genomic, transcriptional, and biochemical analyses. Halomonas sp. 5021 adopts an intact T4LHyp gene cluster containing four enzymes to catabolize T4LHyp into NH₃ and α-ketoglutarate to provide nitrogen and carbon sources for its growth. Compared to Halomonas sp. 5021, Salinicola sp. 4072 lacks an α-KGSA dehydrogenase gene in the T4LHyp gene cluster and can only catabolize T4LHyp into NH₃ and α-ketoglutarate semialdehyde to provide a nitrogen source for its growth. Bioinformatic investigation showed that the 5021-like and 4072-like T4LHyp gene clusters are predominantly found in bacteria from Pseudomonadota, which are widely distributed in multiple marine habitats. Thus, Pseudomonadota bacteria are likely the dominant group to drive the recycling and mineralization of T4LHyp in the ocean.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00272-8.

Zeaxanthin, an oxygenated carotenoid derivative with potent antioxidative properties, is produced by many organism taxa. Flavobacteriaceae are widely distributed in marine environments; however, the zeaxanthin biosynthesis property in this family remains incompletely explored. Here, we characterized zeaxanthin production by marine Flavobacteriaceae strains and elucidated underlying molecular mechanisms. Eight Flavobacteriaceae strains were isolated from the phycosphere of various dinoflagellates. Analyses of the zeaxanthin production in these strains revealed yields ranging from 5 to 3289 µg/g of dry cell weight. Genomic and molecular biology analyses revealed the biosynthesized zeaxanthin through the mevalonate (MVA) pathway diverging from the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway commonly observed in most Gram-negative bacteria. Furthermore, comprehensive genome analyses of 322 culturable marine Flavobacteriale strains indicated that the majority of Flavobacteriaceae members possess the potential to synthesize zeaxanthin using precursors derived from the MVA pathway. These data provide insight into the zeaxanthin biosynthesis property in marine Flavobacteriaceae strains, highlighting their ecological and biotechnological relevance.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00268-4.

Tiny unicellular cyanobacteria or picocyanobacteria (0.5-3 µm) are important due to their ecological significance. Chesapeake Bay is a temperate estuary that contains abundant and diverse picocyanobacteria. Studies of Chesapeake Bay picocyanobacteria in the past 20 years led to the finding of new members of subcluster 5.2 Synechococcus. They laid the foundation for revealing the ecophysiology, biogeography, genomics, and molecular evolution of picocyanobacterial in the Chesapeake Bay and other coastal estuaries. The Bay picocyanobacteria are known to better tolerate the changes in temperature, salinity, and heavy metals compared to their coastal and open-ocean counterparts. Many picocyanobacteria isolated from the Bay contain rich toxin-antitoxin (TA) genes, suggesting that the TA system may provide them with a genetic advance to cope with variable estuarine environments. Distinct winter and summer picocyanobacteria are present in the Bay, suggesting a dynamic seasonal shift of the picocyanobacterial community in the temperate estuary. While the Bay contains subcluster 5.2 Synechococcus, it also contains freshwater Synechococcus, Cyanobium, and marine Synechococcus due to river influx and the ocean's tidal influence. Some Chesapeake Bay picocyanobacterial clades were found in the Bering Sea and Chukchi Sea, showing a link between the Bay and polar picocyanobacteria. Genomic sequences of estuarine picocyanobacteria provide new insight into the taxonomy and evolution of freshwater, estuarine, and marine unicellular cyanobacteria. Estuaries connect freshwater and marine ecosystems. This overview attempts to extend what we learned from Chesapeake Bay picocyanobacteria to picocyanobacteria in freshwater and marine waters.

The interaction of riverine inputs and ocean current systems causes complex spatiotemporal variations in phytoplankton dynamics in marginal seas of the northwest Pacific Ocean, yet quantitative assessments of these variations and their causes remain limited. Here we evaluate phytoplankton biomass and community structure changes using lipid biomarkers, accompanying ocean circulation and nutrient variations in surface waters collected in spring and summer of 2017-2018 at 118 sites in the East China Sea off the Zhejiang coast. High biomass of diatoms, inferred from brassicasterol concentrations, shifted from the south in spring to the north in summer, while high dinoflagellate biomass, inferred from dinosterol concentrations, occurred mainly in the Changjiang (Yangtze) River plume and adjacent areas in both seasons. Seasonal variation in phytoplankton distribution was linked to the spatial extents of water masses such as the Changjiang Diluted Water (CDW) and the intrusion of the Kuroshio Subsurface Water (KSSW). A three end-member mixing model was applied to quantify water mass contributions. The results showed that an increase in the KSSW (from 0 to 40%) and a decrease in the CDW (from 100 to 20%) resulted in a significant (20%) increase in diatom proportions and a significant (20%) decrease in dinoflagellate proportions. Dinoflagellate proportions were highest in the CDW-dominated region, while diatoms and total phytoplankton biomass were higher in the CDW-KSSW mixing region and the KSSW-dominated region. This study highlights the dynamic response of the phytoplankton community to water mass changes in marginal seas that can aid coastal ecosystem management.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00260-y.

Psammophillic ciliates are an integral part of the foodweb despite being underrepresented in terms of molecular phylogeny and modern taxonomy. To investigate the karyorelictean group, sampling was conducted in interstitial marine habitats in China for ciliates living between the sand grains, resulting in an examination of the families Cryptopharyngidae Jankowski, 1980 and Kentrophoridae Jankowski, 1980. Three species, i.e., Cryptopharynx setigerus Kahl, 1928, Kentrophoros fasciolatus (Sauerbrey, 1928) Foissner, 1995 and K. fistulosus (Fauré-Fremiet, 1950) Foissner, 1995, are clearly recognized as being cosmopolitan, while other species await further recording. Phylogenetic analyses were carried out based on updated data. These revealed that the families Cryptopharyngidae and Kentrophoridae are closely related, and most genera studied are monophyletic, although Cryptopharynx qingdaoensis n. sp. is located within the Kentrophoridae branch. Brief revisions of two genera, namely Cryptopharynx Kahl, 1928 and Kentrophoros Sauerbrey, 1928, are provided including keys to the identification of nine species belonging to the former and 12 species belonging to the latter. One new genus, Parakentrophoros n. gen., and one new species, Cryptopharynx qingdaoensis n. sp., are described and a new combination, Parakentrophoros canalis (Wright, 1982) n. comb., is established. Finally, it appears that the subapical oral apparatus undergoes a gradual degeneration process from Cryptopharyngidae to Kentrophoridae.