Marine Life Science & Technology最新文献

Fisheries are social-ecological systems. Evaluating the sustainability of fisheries requires methods to measure performance from ecological, economic, social, and governance aspects. Whereas a number of multi-dimensional evaluation tools such as fishery performance indicators (FPIs) have been used for assessing fishery management systems, fishery management practices and data availability are likely to differ substantially among fisheries in different countries. This makes it at least somewhat problematic to precisely adapt this methodology to fisheries within a given country. This study constructed a practical tool to evaluate and compare fishery systems in China. On the basis of an established indicator library and the FPIs tool, indicators in the newly developed tool for comprehensive fisheries evaluation were selected according to the management objectives, data availability, and the authority of relevant indicators. The sustainability assessment tool for Chinese fisheries (SAT-fish) provides a three-tier hierarchical framework covering 60 indicators, of which 48 indicators were extracted from the FPIs tool and 12 indicators were associated with policy statements. Applicability and comprehensiveness of this tool in comparison with six other well-established frameworks were investigated. This tool offers a promising new method to assess the sustainability of fishery systems in China, with great potential to guide Chinese fisheries towards a higher level of sustainability.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00251-z.

Genomic selection (GS) applied to the breeding of aquatic animals has been of great interest in recent years due to its higher accuracy and faster genetic progress than pedigree-based methods. The genetic analysis of complex traits in GS does not escape the current excitement around artificial intelligence, including a renewed interest in deep learning (DL), such as deep neural networks (DNNs), convolutional neural networks (CNNs), and autoencoders. This article reviews the current status and potential of DL applications in phenotyping, genotyping and genomic estimated breeding value (GEBV) prediction of GS. It can be seen from this article that CNNs obtain phenotype data of aquatic animals efficiently, and without injury; DNNs as single nucleotide polymorphism (SNP) variant callers are critical to have shown higher accuracy in assessments of genotyping for the next-generation sequencing (NGS); autoencoder-based genotype imputation approaches are capable of highly accurate genotype imputation by encoding complex genotype relationships in easily portable inference models; sparse DNNs capture nonlinear relationships among genes to improve the accuracy of GEBV prediction for aquatic animals. Furthermore, future directions of DL in aquaculture are also discussed, which should expand the application to more aquaculture species. We believe that DL will be applied increasingly to molecular breeding of aquatic animals in the future.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00252-y.

Determining and comparing mitochondrial genomes (mitogenomes) are essential for assessing the diversity and evolution of mitochondria. Ciliates are ancient and diverse unicellular eukaryotes, and thus are ideal models for elucidating the early evolution of mitochondria. Here, we report on six new mitogenomes of spirotrichs, a dominant ciliate group, and perform comparative analyses on 12 representative species. We show that: (1) the mitogenomes of spirotrichs are linear structures with high A+T contents (61.12-81.16%), bidirectional transcription, and extensive synteny (except for the nad5, ccmf and cob genes in Euplotia); (2) the non-split of NADH dehydrogenase subunit 2 gene (nad2) is a plesiomorphy of ciliates, whereas it has evolved into a split gene in Spirotrichea (apart from Euplotes taxa), Oligohymenophorea, and Armophorea; (3) the number of small subunit ribosomal proteins (rps) encoded in mitogenomes increases in the later branching classes of ciliates, whereas rps8 shows a loss trend during the evolution of Euplotes taxa; (4) the mitogenomes of spirotrichs exhibit A/T codon bias at the third position, and the codon bias is mainly due to DNA mutation in oligotrichs, hypotrichs and Diophrys appendiculata; (5) the phylogenetic position of D. appendiculata is unstable and controversial based on both phylogenetic analyses and mitogenome evidence. In summary, we investigated the mitogenome diversity of spirotrichs and broadened our understanding of the evolution of mitochondria in ciliates.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00249-7.

Bioluminescence, the ability of organisms to produce visible light, has intrigued scientists for centuries. Studies have examined bioluminescence, using a wide range of approaches and organisms, from its ecological role to its underlying molecular mechanisms, leading to various applications and even a Nobel prize. Over the last ten years, an increasing amount of data has been collected leading to a growing number of recognized marine bioluminescent species. This review provides and describes a referenced listing of the eukaryotic luminous marine species, including information related to: (i) intrinsic versus extrinsic source of the bioluminescence, (ii) the color and maximum wavelength of emission, (iii) the bioluminescent system (substrate and enzyme) and the associated molecules, (iv) the availability of light organ/cell(s) pattern and histological structure, (v) the physiological control of the light production, and (vi) the demonstrated or suggested bioluminescent function(s). This listing provides basic information and references for researchers in or entering in the field of marine bioluminescence. Using a semi-quantitative approach, we then highlight major research gaps and opportunities and reflect on the future of the field.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00250-0.

Aquaculture is critical to reduce protein deficiencies and supplement the world's demand for seafood. However, the culture environment predisposes farmed animals to infectious diseases. In particular, the high density of fish, crustacean, mollusk, sea cucumber or algal species allows for the rapid spread of infectious diseases resulting in devastating losses. Massive amounts of antibiotics have been used to sustain aquaculture production. This has led to the critical need to evaluate the impact of current control measures and optimize disease management schemes with an emphasis on global impact and sustainability. Furthermore, local and global changes have enhanced the pathogens' effects over aquaculture settings because increased temperature and pollution may trigger virulence genes and toxin production. Technological developments including biofloc technology, integrated multitrophic systems, recirculating aquaculture systems and probiotics have contributed to enhancing aquaculture sustainability and reducing the need for high loads of antibiotics and other chemicals. Furthermore, biotechnological tools (e.g., omics and cell biology) have shed light on cellular processes in the health and disease of reared organisms. Metagenomics is a reliable and relatively quick tool to identify microbial communities in aquaculture settings.

Ciliates in the subclass Hypotrichia have long been difficult to classify as they are one of the most polymorphic and highly differentiated groups, leading to their systematics remaining unresolved. Phylogenetic relationships within the hypotrich family Strongylidiidae have been ambiguous due to discordance between the morphological and genetic data. In this study, a new strongylidiid genus Heterouroleptus is established, mainly based on the novel mode of origin of the ventral cirral rows: left ventral cirral row (LVR) originates from frontal-ventral-transverse cirral anlagen (FVTA) III (anterior portion), IV (middle portion), and V (rear portion); right ventral cirral row comes from the entire FVTA VI. A new species, Heterouroleptus weishanensis gen. nov., sp. nov., is investigated along with the morphometric and molecular data from a population of Strongylidium wuhanense. Eight new sequences and nuclear gene markers (single-gene and multi-gene) are provided to analyze the phylogenetic relationships of strongylidiids, with the COI gene utilized to uncover further genetic information at species level and below. The results reveal that: (1) Strongylidiidae is monophyletic and has a close relationship with Dorsomarginalia; (2) Heterouroleptus gen. nov. forms a clade that is sister to all the other strongylidiids; (3) Hemiamphisiella Foissner, 1988 and Pseudouroleptus Hemberger, 1985 should not be synonyms, and both genera should be subdivided due to their variable morphological characteristics; (4) LVR originating from three anlagen is a plesiomorphy of Strongylidiidae. The discovery of the origin of the LVR not only contributes to the establishment of the genus Heterouroleptus, but also helps to improve the diagnosis of the family Strongylidiidae.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00243-z.

Vaccines are one of the most practical means to stop the spreading of Aeromonas veronii in aquaculture. In this study, virulence factor aerolysin mutant NTaer which has lost its hemolytic activity was used as a target antigen. Pichia pastoris constitutive secretory expression NTaer (GS115-NTaer) was used as a potential safe oral vaccine to evaluate its effectiveness on zebrafish immunity. The result shows that vaccination of GS115- NTaer for four weeks did not affect the growth performance of the host, while eliciting an effective immune protective response. Compared with the control group, the GS115-NTaer could significantly up-regulate the relative expression level of the intestinal tight junction protein 1α (TJP1α) gene, and significantly increased the contents of lysozyme (LYZ), complement C3 and C4 in the gut, indicating that the innate immune response of the fish was activated. The relative gene expression levels of macrophage-expressed gene 1 (MPEG1) and T cell receptor (TCR-α) in the gut, and MPEG1, CD4, CD8, TCR-α, GATA3, and T-bet in the spleen were all increased significantly, indicating that the cellular immune response of the fish was activated. Furthermore, the contents of serum IgM and intestinal mucosa IgZ antibodies were significantly increased, which showed that humoral immunity was also activated. Moreover, inoculation with GS115-NTaer significantly changed the structure of gut microbiota. In particular, the relative ratio of (Firmicutes + Fusobacteriota + Bacteroidota)/Proteobacteria was significantly higher than that of the control and GS115 groups. Lastly, the vaccinated fish were challenged with A. veronii, and the relative percent survival of GS115 and the GS115-NTear groups was 14.28% and 33.43%. This improvement of immunity was not only due to the specific immune response but also attributed to the improvement of innate immunity and the gut microbiota which was demonstrated by the germ-free zebrafish model. Collectively, this study provides information on the effectiveness of GS115-NTear as an oral vaccine for the green prevention and control of A. veronii infection in fish aquaculture.

The aquatic plant Nymphaea, a model genus of the early flowering plant lineage Nymphaeales and family Nymphaeaceae, has been extensively studied. However, the availability of chloroplast genome data for this genus is incomplete, and phylogenetic relationships within the order Nymphaeales remain controversial. In this study, 12 chloroplast genomes of Nymphaea were assembled and analyzed for the first time. These genomes were 158,290-160,042 bp in size and contained 113 non-repeat genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. We also report on codon usage, RNA editing sites, microsatellite structures, and new repetitive sequences in this genus. Comparative genomics revealed that expansion and contraction of IR regions can lead to changes in the gene numbers. Additionally, it was observed that the highly variable regions of the chloroplast genome were mainly located in intergenic regions. Furthermore, the phylogenetic tree showed the order Nymphaeales was divided into three families, and the genus Nymphaea can be divided into five (or three) subgenera, with the subgenus Nymphaea being the oldest. The divergence times of nymphaealean taxa were analyzed, with origins of the order Nymphaeales and family Nymphaeaceae being about 194 and 131 million years, respectively. The results of the phylogenetic analysis and estimated divergence times will be useful for future evolutionary studies of basal angiosperm lineages.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00242-0.

Traditional cultivation methods with defined growth media can only isolate and cultivate a small number of microbes. However, much higher microbial diversity has been detected by cultivation-independent tools from a range of natural ecosystems. These represent a large unexplored pool of potentially novel taxa. In this study, a diffusion-based integrative cultivation approach (DICA) was developed to efficiently isolate novel taxonomic candidates from marine sediment. DICA combined a newly designed diffusion-based apparatus called a "microbial aquarium" with modified low-nutrient media. To determine the efficiency of DICA, cultivation results were compared with traditional cultivation approach (TCA). Both cultivation approaches resulted in the isolation of numerous representatives from the phyla Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota. However, the newly developed DICA also led to the successful cultivation of species from rarely cultivated phyla such as Verrucomicrobiota and Balneolota. Based on 16S rRNA analyses, the application of DICA resulted in the successful cultivation of 115 previously uncultured taxa out of a total of 196 isolates. Among these, 39 were identified at the genus level and 4 at the family level, showcasing a novelty ratio of 58%. Conversely, the TCA cultivated 12% (20/165) of novel isolates, with all at species level only. The isolated microbial diversity showed that species recovered by DICA belong to 12 different classes, twice the number produced by TCA. Overall, these results demonstrate that the newly designed DICA produces a high recovery of diverse and previously uncultured bacteria.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00240-2.

As one of the common malignancies that threaten human life, bladder cancer occurs frequently with a high mortality rate in the world, due to its invasion, recurrence and drug resistance. Natural products from marine microorganisms are becoming the hotspots in discovery of new candidate drug entities, especially in the area of cancer. Brefeldin A (BFA) is a natural Arf-GEFs inhibitor, but due to the low aqueous solubility, strong toxicity, and poor bioavailability, it is urgent to conduct structural optimization research. Herein, a new BFA pyridine acrylate derivative CHNQD-01281 with improved solubility was prepared and found to exert moderate to strong antiproliferative activity on a variety of human cancer cell lines. It was noteworthy that CHNQD-01281 was most sensitive to two bladder cancer cell lines T24 and J82 (IC₅₀ = 0.079 and 0.081 μmol/L) with high selectivity index (SI = 14.68 and 14.32), suggesting a superior safety to BFA. In vivo studies revealed that CHNQD-01281 remarkably suppressed tumor growth in a T24 nude mice xenograft model (TGI = 52.63%) and prolonged the survival time (ILS = 68.16%) in an MB49 allogeneic mouse model via inducing infiltration of cytotoxic T cells. Further mechanism exploration indicated that CHNQD-01281 regulated both EGFR/PI3K/AKT and EGFR/ERK pathways and mediated the chemotactic effect of chemokines on immune effector cells. Overall, CHNQD-01281 may serve as a potential therapeutic agent for bladder cancer through multiple mechanisms.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-024-00246-w.