Cyrtophorians are a diverse and ecologically important group of protists, playing multiple roles in aquatic ecosystems. However, studies on the subclass Cyrtophoria remain limited, resulting in persistent confusion regarding their taxonomy, phylogeny and distribution. Three cyrtophorians isolated from the Yangtze Estuary, namely Monochilodonella sinica gen. et sp. nov., Chlamydonella foissneri sp. nov. and Gastronauta derouxi Blatterer & Foissner, 1992, were investigated using an integrative morpho-molecular approach. Monochilodonella sinica gen. et sp. nov. possesses a single circumoral kinety, which indicates that it represents a new lineage of Chilodonellidae. Both the secondary structure of the nuclear SSU rRNA molecule and the phylogenetic analyses place this new genus within Chilodonellidae, closely related to Pseudochilodonopsis. Chlamydonella foissneri sp. nov. clusters with Chlamydonellopsis species rather than its congeners, rendering both Chlamydonella and Chlamydonellopsis non-monophyletic. After briefly reviewing the family Chilodonellidae, we propose a hypothetical evolutionary trajectory for the family Chilodonellidae based on both morphological and molecular data. Furthermore, illustrated identification keys are provided for the genera of Chilodonellidae and for species of Chlamydonella.

Marine anoxic sediments are expansive ecosystems, effectively devoid of oxygen, where eukaryotic life is predominantly represented by protists. In this study, we surveyed a range of such habitats and uncovered novel diversity within ciliated protists from the subclass Scuticociliatia (class Oligohymenophorea). We establish three new genera of marine anaerobic scuticociliates within the family Anaerocyclidiidae that were previously detected exclusively through cultivation-independent environmental surveys. Our results show that marine Anaerocyclidiidae have a global distribution and occur frequently in anoxic sediments. Notably, all studied marine Anaerocyclidiidae host prokaryotic ectosymbionts of varying sizes and shapes, potentially representing distinct prokaryotic lineages. Through broad geographic sampling and the establishment of the largest culture collection of marine anaerobic scuticociliates to date, we investigated the diversity, morphology, behavior, and symbiotic associations within this significant ciliate lineage. These findings highlight the importance of cultivation approaches to uncover novel protistan taxa and their symbiotic relationships, expanding our understanding of biodiversity and ecosystem functioning in oxygen-depleted habitats.

Ciliates are an ancient and highly diverse group of unicellular eukaryotes that hold significant value in various fields of research such as ecology, evolutionary biology, and epigenetics. With the advancement of sequencing technology and deeper research into ciliates, an increasing amount of omics data have been generated. Here we compiled high-throughput sequencing data from 96 functional gene knockdown or knockout experiments in three genetically manipulable model ciliates, Tetrahymena thermophila, Paramecium tetraurelia, and Oxytricha trifallax, as well as other omics data from 69 ciliate species, to establish a functional genomics database for ciliates (CiliateBase; available at http://ciliatebase.maolab.org/). CiliateBase integrates various data types, including RNA-seq, ChIP-seq, MNase-seq, and RIP-seq, to analyze the functional genes and regulatory networks in ciliates. It provides tools for gene expression analysis, Gene Ontology (GO) enrichment analysis, and KEGG pathway enrichment analysis. With its user-friendly interface and powerful data visualization tools, CiliateBase enables researchers to easily search and analyze functional genomics data. It also supports downloading raw data and processed results, significantly facilitating the progress of ciliate research. In summary, CiliateBase provides a robust resource for functional genomics studies of ciliates.

Odontostomatid ciliates, known for over a century, were historically classified within various taxonomic groups of Ciliophora Doflein, 1901 until their reclassification into the class Odontostomatea. Despite the recognition of 25 valid species, most descriptions predate the advent of silver impregnation and sequencing methods. Consequently, many species were described based solely on observations of live specimens, leading to incomplete or ambiguous records. To date, redescriptions of only three species include 18S rRNA gene sequences data, and their evolutionary relationships remain unresolved. In this study, we investigated 32 populations representing 15 species—including three newly described—across the genera Discomorphella, Epalxella, Limnomylestoma gen. nov., Mircalla gen. nov., Mylestoma, Pelodinium, Saprodinium, and Tostonella gen. nov. Comprehensive analyses were conducted using in vivo microscopy, silver impregnation, and scanning electron microscopy. We also designed specific primers to amplify the partial 18S rRNA gene of various odontostomateans and retrieved additional 18S rRNA sequences from environmental metatranscriptomic and metagenomic datasets. This study represents the most extensive investigation of Odontostomatea to date, confirming the monophyly of the class by revealing the position of Epalxella, reconstructing its internal phylogeny, identifying two main odontostomatean lineages, and revealing its remarkable diversity.

Histone H3 clipping, a unique but evolutionarily conserved post-translational modification that irreversibly removes the N-terminal tail of H3, has been reported across diverse eukaryotic lineages. In Tetrahymena thermophila, a ciliate with nuclear dimorphism, H3 clipping is a bona fide proteolytic event generating H3^F (H3-Fast) by removing the first six N-terminal amino acids, specifically in the transcriptionally silent micronucleus (MIC). However, the detection of H3^F remains technically demanding, time-consuming, and lacks spatio-temporal resolution. To overcome this, a 2 × branched peptide antigen was developed to generate a high-specificity antibody that exclusively recognizes H3^F, effectively distinguishing it from full-length H3 and other truncation variants. This antibody eliminated the need for labor-intensive MIC isolation and histone extraction, enabling rapid, small-scale detection directly from whole-cell lysates. Using this antibody, dynamic subcellular localization of H3^F was investigated through different cell stages, revealing its persistence during vegetation, starvation and early conjugation. However, H3^F disappeared concurrently with macronuclear anlage formation, supporting the notation that removal of H3^F is a prerequisite for the new macronucleus development. Comparative analyses further revealed that H3 Ser10 phosphorylation, though previously used as an alternative H3^F marker, actually occurs strictly after clipping, refining the temporal hierarchy of these two chromatin events. This work provides the first in situ, high-resolution method to track endogenous H3 clipping, providing both a technical platform and new biological insight into the developmental regulation of proteolytic histone modifications.

With a total of 33 genera, the family Folliculinidae Dons, 1914 represents the most genus-rich lineage within the class Heterotrichea. Its members are characterized by a transparent lorica, conspicuous peristomial lobes, and a dimorphic life cycle, which distinguishes them from other heterotrichs. Although approximately 80 nominal species have been recognized within the family, most aspects of their morphology, life cycle, and molecular information are still unknown. In the present study, a new species, Metafolliculina songi n. sp., collected from a wetland in China, is investigated using morphological and molecular methods. The complete life cycle and morphology of this species are documented, along with detailed ecological information and cultivation protocols. Notably, this folliculinid exhibits unique vulnerabilities: its short, wide neck and lack of a closure mechanism make it susceptible to predation by the ciliate Loxophyllum salinum and infestation by rotifers. Phylogenetic analysis based on small subunit ribosomal DNA (SSU rDNA) sequences confirms the monophyletic nature of the family Folliculinidae. However, M. songi n. sp. unexpectedly formed a sister relationship with Metafolliculina +  Eufolliculina, suggesting evolutionary relationships within this family require further investigation through additional data.

Lateral gene transfer (LGT) is a key driver of evolutionary innovation, underlying protists’ lifestyles and interactions in anaerobic environments. Yet, its significance in free-living protists remains underexplored. Here, we address this gap by presenting the first single-cell transcriptomes of Metopus yantaiensis and genome-wide LGT screens across 36 omics datasets from nine anaerobic APM ciliates (classes Armophorea, Muranotrichea, and Parablepharismea)—a group in soil/sediment environments. Through phylogenetic analyses and validation testing, we identified 63 candidate prokaryotic LGT genes preferentially enriched in APM ciliates. Among these, 19 form interconnected pathways for degrading complex organics (polysaccharides, amino sugars); their high diversity and completeness are rarely seen in reported protist LGTs. A rare fused gene (arcC-OTC) and two novel genes (acs, ME2) were exclusively identified in APM ciliates, with their potential as the first evidence of LGT-mediated carbon metabolite retention and ammonia assimilation in phagotrophic protists inferred. Notably, 27 LGTs (including arcC-OTC, acs, and ME2) trace to candidate phyla radiation (CPR) bacteria or described prokaryotes, marking the first CPR-to-eukaryote LGT documentation. Collectively, these 63 LGTs are predicted to enhance nutrient utilization (complex organics, other carbon metabolites, inorganic elements), bioenergetic efficiency, and stress resistance (heavy metals, oxygen), facilitating soil/sediment adaptation. Overall, our results highlight lateral prokaryotic gene acquisition may be key for free-living anaerobic ciliates’ adaptation to new environments, shedding light on protists’ evolutionary dynamics and ecological roles.

In the mantle cavity of the heterobranch snail Physella acuta, collected from a lake in Slovakia (Central Europe), we identified the peritrich ciliate Trichodina chlorophora harboring endosymbiotic green algae. To elucidate the evolutionary origins of this tripartite consortium, we determined the phylogenetic affiliations of all three partners and conducted a detailed morpho-molecular characterization of the ciliate, a central component of this hyper-symbiotic system. The European population of T. chlorophora closely matched North American populations previously described from physinine snails. The diagnostic features of T. chlorophora include: body diameter of 41–83 μm after dry silver nitrate impregnation; denticle ring 23–39 μm wide, with 23–30 denticles and 9–11 radial pins per denticle; denticles 5.7–7.8 μm long; adoral ciliary spiral performing ~ 1.13 turns (390°–409°) around peristomial disc; and a horseshoe-shaped macronucleus. Phylogenetic analyses revealed that: (1) the host snails are closely related to North American conspecifics, reflecting the human-mediated introduction of this invasive gastropod to Europe; (2) trichodinids colonized aquatic snails multiple times independently from poikilothermic vertebrate hosts, with T. chlorophora clustering with freshwater congeners from frogs, snails, and planarians; and (3) the endosymbiotic green algae comprise two species: Chlorella sp., closely related to endosymbionts of heliozoans and cnidarians, and Jaagichlorella geometrica, which clusters with epiphytic congeners. While the algae exhibit low host specificity, snail-dwelling Trichodina species show high phylogenetic host specificity. The parallel emergence of green algae-bearing trichodinids in physinine and planorbid snails suggests co-evolutionary processes that independently gave rise to interdependent associations among aquatic snails, ciliates, and zoochlorellae.

Meiosis is regulated by phase-specific genes to orchestrate nuclear and cytoskeletal dynamics essential for sexual reproduction. The ciliate Paramecium tetraurelia exhibits nuclear dimorphism, harboring two germline micronuclei (MICs) and one somatic macronucleus (MAC) within a single cell during vegetative growth. During sexual reproduction, the MICs undergo meiosis and the MAC deforms and fragments, providing a unique model to study the regulation of diverse nuclear events. Transcription factor DP (TFDP), which heterodimerizes with E2Fs, can bind to specific DNA motifs in promoters of cell cycle-regulated genes to activate or repress their expression. Here, we identified 16 TFDP homologs in P. tetraurelia, representing an exceptional gene family expansion accompanied by functional domain diversification. The functions of Tfdp1a and Tfdp1b, which are specifically expressed during sexual reproduction and localize in the old and new MACs, were further investigated. Their depletion resulted in meiotic arrest at metaphase in the MIC, failure of old MAC fragmentation, and abortive cytokinesis. Transcriptomic analysis revealed that TFDP1A/1B knockdown primarily causes gene downregulation, with > 60% of downregulated genes being specifically highly expressed during sexual reproduction. Functional annotation and enrichment analyses demonstrated significant downregulation of proteins involved in meiosis, DNA replication, and DNA repair. Critically, multiple downregulated meiotic regulators are essential for proper homologous chromosome segregation and sister chromatid separation, providing a mechanistic basis for the observed MIC meiotic arrest. This study uncovers Tfdp1a/1b as essential regulators of the distinctive meiotic process in P. tetraurelia, providing crucial insights into nuclear dynamics and the regulation of sexual reproduction in binucleate systems.

Vanadium-dependent haloperoxidases (vHPOs) are essential enzymes in macroalgae, known for their ability to catalyze halogenation reactions using halides and hydrogen peroxide. These enzymes facilitate the biosynthesis of halogenated compounds that contribute to the defense mechanisms of algae and are considered to play a crucial role in the oxidative stress response. Using a transcriptomic approach, we discovered and analyzed about 70 novel vHPO sequences from nine different macroalgae species collected in the Baltic Sea. All sequences were carefully selected for their universal catalytic center characterized by structurally conserved residues essential for catalysis and vanadate-binding. Mass spectrometry provided evidence for eight of those proteins in extract fractions of the brown alga Saccharina latissima. Using RT-qPCR, we also investigated the role of vHPO gene expression in stress response on a subset of S. latissima vHPO transcripts by exposing it to different stressors including copper excess, oxidative stress, and biotic stress mimicked by elicitor treatment using a S. latissima tissue homogenate. The optimal quantum yield of photosystem ll served as a physiological plant stress parameter (F_V/F_M). Our data support the hypothesis that these enzymes are involved in mitigating oxidative stress, as suggested by up-regulation in gene expression following H₂O₂ and elicitor treatments, and are likely involved in environmental stress response. This work advances our understanding of vHPO function in marine algae and highlights their potential role in responding to environmental stress.

Global warming may drive adaptive evolution by influencing natural selection and utilizing temperature-related phenotypic plasticity. However, predicting the evolutionary patterns of phenotypic plasticity under climate change remains a challenge, underscoring the need to elaborate on the underlying genetic and molecular mechanisms. In this study, we focus on the expression plasticity divergence of heat shock protein 90 (Hsp90), which is temperature responsive and exhibits a strong selective sweep in the upstream noncoding region of two allopatric congeneric oyster species: cold-adapted Crassostrea gigas and warm-adapted Crassostrea angulata. Functional characterization confirmed Hsp90 expression as an ideal proxy for thermotolerance. The evolutionary divergence in constitutive and plastic expression patterns represents adaptation to the mean and variance in habitat temperature, respectively. By combining forward and reverse genetic approaches, four causative loci with G + G × E effects were identified in the Hsp90 promoter regions of C. gigas and C. angulata, indicating cis-variations. Moreover, the g.-2291G allele of the causative locus in C. angulata is specifically bound to by the positive transcription factor purine-rich element binding protein B (PURB), explaining the constitutive expression of Hsp90. Meanwhile, the response of PURB to thermal stress determines the magnitude of plastic Hsp90 expression in C. angulata. This integrative study revealed that cis-variations interact with trans-variations and underlie the G × E effect under environmental changes, thereby mediating the divergence in plastic gene expression. Furthermore, we established a paradigm for studying genetic variants and their G × E impacts at a finer resolution, i.e., single-nucleotide level, in nonmodel organisms. The findings may deepen our understanding of the significant role of phenotypic plasticity in modulating adaptive responses and promote predictions of adaptive potential in marine organisms under climate change.

In terrestrial animals, the somatotropic axis, comprising growth hormone (GH) and insulin-like growth factors (IGFs), is pivotal in regulating growth and development. Marine mollusks play a vital role in the aquaculture industry, and understanding the molecular mechanisms of mollusk growth is of great value to breeding fast-growing and high-yielding varieties. Unlike terrestrial animals, marine mollusks lack a model species for laboratory breeding, leaving many growth-related genes unvalidated. The dwarf surf clam Mulinia lateralis, with its small size, short breeding cycle, and ease of cultivation in laboratory settings, serves as an ideal model for investigating growth regulation. This study is the first systematic identification of genes related to M. lateralis growth, with 195 differentially expressed genes (DEGs) being found between fast- and slow-growing individuals through transcriptome comparison. KEGG analysis revealed significant enrichment of the insulin-like signaling pathway, and the insulin-like peptide (ILP) was the most significantly upregulated. As the insulin signaling pathway is activated by ligand–receptor binding, we further characterized and functionally validated mlILP and its receptor, the insulin receptor-related receptor (mlIRR). RNA interference (RNAi)-mediated knockdown of mlILP or mlIRR resulted in growth retardation, confirming their positive roles in growth regulation. Notably, silencing of these two genes caused significant upregulation of downstream genes, suggesting a compensatory mechanism for maintaining cell homeostasis. Our findings advance the understanding of growth regulation in mollusks and provide candidate genes for scallop breeding aiming at growth improvement.

Freshwater turtles are one of the most threatened animal groups in the world, especially in Asia. The Beale’s Eyed Turtle (Sacalia bealei) is a highly endangered Chinese species at risk of extinction due to overexploitation for the food and pet trades. Nonetheless, Hong Kong still houses a handful of relatively healthy populations of this species, providing an increasingly rare opportunity to study the population genetics of wild populations and, in turn, guide conservation action. In this study, we used genome-wide double-digest restriction-site associated DNA sequencing (ddRADseq) markers to examine the population structure of S. bealei from all known wild individuals with samples suitable for DNA sequencing, representing a subset of its distribution in Hong Kong (two localities: HK1, HK2) and Fujian Province. Although genetic diversity is relatively low, we recovered four genetic clusters, with three corresponding to each of the three known localities (HK1, HK2, Fujian), and admixture between the clusters. Captive-breeding colony individuals showed mixed geographic origins, with approximately half clustering with Fujian populations and half with Hong Kong populations. These data were used to evaluate the genetic diversity and infer the geographic origin of an ex situ breeding colony with individuals of unknown provenance. These results provide important baseline information on the population structure of wild S. bealei and the potential geographic origins of captive turtles, which directly contribute to in situ and ex situ conservation efforts of the species.

Mammalian microfold cells (MCs) are specialized epithelial cells (ECs) that initiate mucosal immune responses through the uptake and transcytosis of luminal antigens. However, such type of antigen-sampling cells remains largely unknown in teleost fish. In this study, the lectins Ulex europaeus agglutinin-1 (UEA-1) and wheat germ agglutinin (WGA), as well as the monoclonal antibody (mAb) NKM-16-2-4 raised against mouse MCs, were used to identify the MCs in the intestines of olive flounder (Paralichthys olivaceus). These cells exhibit binding characteristics with UEA-1 and mAb NKM-16-2-4, similar to mammalian MCs, and were negative for acid and alkaline phosphatase staining. In addition, unique NKM-16-2-4⁺/WGA⁺ or UEA-1⁺/WGA⁺ cells were also identified. The UEA-1⁺ (including UEA-1⁺/WGA⁺) cells of the anterior, mid, and posterior intestines could take up inactivated Vibrio anguillarum and fluorescent microspheres. These were transported across the epithelium to the underlying lamina propria. Consequently, we renamed these UEA-1⁺ cells as MCs. The MCs of flounder showed short and irregular microvilli, without a mammalian-type basal pocket-like structure, but macrophages and lymphocytes at their basal areas. Co-staining confirmed that the flounder MCs lacked MHC II expression, and that MHC II⁺, IgM⁺ B, and CD83⁺ dendritic cells were underneath or adjacent to the MCs. After oral administration, inactivated V. anguillarum were detected in the MHC II⁺ cells at 6 h. These results indicated that the MCs in teleost intestines act as entry points within the epithelial barrier for particulate antigens. They also provide data valuable for developing novel mucosal vaccines targeting the MCs in teleosts.

Coral reef fish exhibit vivid carotenoid-based coloration that plays an important role in communication and camouflage within the complex reef ecosystems. However, the molecular mechanisms underlying carotenoid coloration in these fish remain elusive. In this study, we explored the color differentiation process in Plectropomus leopardus, induced by dietary carotenoid intake, using integrated histological observations and multi-tissue transcriptomic analyses. We found that individuals with red coloration (B-AX-R) displayed an increased capacity for carotenoid absorption, transport, and deposition, along with enhanced melanin removal; however, in non-reddened individuals (B-AX-B), carotenoids were primarily used for immunity and other cellular processes rather than pigmentation. Notably, scavenger receptor Class B member 2c (scarb2c) emerged as a key gene responsible for coloration by regulating pathways involved in carotenoid uptake and transport, with interactions involving Apolipoprotein A-I (APOA1), Apolipoprotein A-IV (APOA4), and Apolipoprotein E (APOE). Through integrated metabolomics, the molecular mechanism underlying carotenoid coloration was revealed, in which scarb2c mediates a regulatory network that coordinates key metabolites, including 5b-Cyprinol, KAKA, and creatine, along with other genes involved in absorption and transport. These findings provide the first comprehensive insight into carotenoid coloration in coral reef fish and contribute to our understanding of the signaling functions associated with coloration in coral reef ecosystems.

The significantly negative impact of marine invasive species underscores the need to understand the dynamics of invasion success. MicroRNAs (miRNAs) play a crucial role in regulating gene expression in response to stresses during invasions. Using the invasive tunicate Ciona robusta as a model, here we aim to study intragenic miRNA–host gene co-expression and functional regulation in response to recurrent salinity challenges. Despite genomic nestedness, only 9% of miRNA–host gene pairs showed significant co-expression (p < 0.05, correlation coefficient > 0). Recurring stresses dynamically altered the co-expression, revealing distinct miRNA–host gene expression at different stress times and stages. These differentially expressed miRNAs (p_adj < 0.05, |log₂foldchange|> 1) regulated biological processes, including free amino acid metabolism, water channel function, and ion transport to maintain osmotic homeostasis. These functional regulations were specific to time and stage, targeting the same type of osmolytes through varied pathways. Our findings highlight the diverse regulatory roles of miRNAs in enabling rapid responses to environmental stresses during invasions, providing new insights into miRNA-driven phenotypic plasticity under changing conditions.

Mussels fabricate byssus to anchor themselves on diverse substrates, a process that is crucial for their survival in dynamic marine environments, as well as for aquaculture productivity. Currently, many studies have focused on the composition of mussel adhesive proteins (MAPs) and their self-assembly in vivo and in vitro. However, the biological regulation of byssus fabrication other than MAPs has been largely overlooked. Given the established roles of Ca in cellular regulation, as well as its frequent detection in byssus and the environment, Ca (50 mmol/L) was applied as an environmental stimulus to investigate the regulatory mechanisms of byssus in thick-shelled mussels, Mytilus coruscus. After 7 days of exposure, the secretion behavior of mussels, histology of the three foot sections (anterior, middle, and posterior), anterior-section transcriptomics, and section-specific gene expression were integratively analyzed. The results revealed that Ca exposure inhibited macroscale byssus self-assembly, but the self-assembly of microscale byssus precursors and histological status in the different foot sections were not affected. Moreover, no negative effects on MAP expression were identified. However, the cytoskeleton-based secretory process became imbalanced, and the gene expression in the three foot sections was disordered (e.g., genes encoding actin, tubulin, and calponin). In addition, Ca-induced foot paralysis may be accompanied by negatively regulated neurotransmission and muscle contraction, which may account for the absence of macroscale byssus. Overall, this study demonstrated that MAPs were not decisive in the self-assembly of byssus. Other biological regulatory processes, as well as the spatial heterogeneity of the mussel foot, should be considered when exploring the self-assembly mechanisms of byssus. This may then provide cues for mussel aquaculture and the development of novel biomimetic materials.

Pacific cod (Gadus macrocephalus) and walleye pollock (Gadus chalcogrammus) are commercially important species in bottom trawl fisheries in Japanese waters. However, their first-year life history processes and whether current management units align with the scale of their biological processes remain unclear. To investigate this, we conducted otolith macrostructural analysis on age-1 Pacific cod and walleye pollock collected from the Pacific Ocean off Hokkaido, Aomori Prefecture, and Sendai Bay (Honshu). Stable isotope analysis (δ¹³C, δ¹⁸O) was performed on both the inside and outside of the otolith check using isotope ratio mass spectrometry (IRMS) and secondary ion mass spectrometry (SIMS). The δ¹⁸O shift across the check, combined with higher δ¹³C and δ¹⁸O values on the outside of the check compared to the inside, suggests that both species undergo a habitat transition during their first-year settlement. Stock discrimination was more successful for individuals from Hokkaido and Sendai Bay than for those from Aomori Prefecture. When isotope data from the two southern regions (Aomori Prefecture and Sendai Bay) were combined into a single Honshu stock, the overall classification success increased from 71 to 76%, with Cohen’s Kappa (κ) rising significantly from 0.31 to 0.60. These results indicate that managing stocks based on geographic distribution is both scientifically valid and practical though inter-stock admixture should be taken into account. Overall, otolith stable isotope analysis proves to be a valuable tool for identifying key life history events, stock structure, and migration patterns in these gadoid species.

Lectins are carbohydrate-binding proteins that function as pattern recognition receptors (PRRs) in animal innate immune system. Although invertebrates like mussels lack adaptive immune cells, they still mount pathogen-specific responses through rapidly recognition of pathogen-associated molecular patterns (PAMPs) by PRRs. Here, we identify and characterize a galactose-binding lectin from Mytilus coruscus, MytiGal, which belongs to the Mytilectin family. MytiGal features a β-trefoil fold with conserved carbohydrate-binding sites and shares significant homology with lectins in other marine bivalves. It is highly expressed in the foot, mantle, and hemocytes, and its expression is significantly upregulated following bacterial challenge. Functional assays using recombinant MytiGal revealed its capacity to bind carbohydrates, broad-spectrum antimicrobial activity, and bacterial binding and agglutination activities. Additionally, MytiGal enhanced hemocyte phagocytic activity and facilitated bacterial clearance both in vivo and in vitro. It also alleviated bacteria-induced vacuolation and activated the antibacterial autophagy of hemocytes by regulating the autophagy pathway and the TLR/NFκB signaling pathway. These findings suggest that MytiGal plays a critical role in the immune response of mussels via the activation of antibacterial autophagy and provide new insights into the immune recognition mechanisms in marine bivalves.

Gracilariopsis lemaneiformis is the second most cultivated seaweed in China. In this study, the role of polyamines (PAs) in promoting carpospore release in G. lemaneiformis was investigated. The results showed that 300 μmol/L PAs (putrescine:spermine:spermidine 1:1:1) effectively increased carpospore release in G. lemaneiformis. Exogenous PAs influenced the photosynthetic system of G. lemaneiformis, with the photosynthetic capacity decreasing on the third day but largely recovering on the seventh day. Moreover, the contents of phycoerythrin (PE) and chlorophyll a (Chl a) significantly increased after three days. Additionally, the level of reactive oxygen species (ROS) significantly increased after PAs stimulation, and the activities of antioxidant enzymes and levels of antioxidant substances, such as superoxide dismutase (SOD), peroxidase (POD), malate dehydrogenase (MDH), catalase (CAT), glutathione (GSH), and malondialdehyde (MDA), also changed accordingly. The increase of auxin, cytokinin, and salicylic acid contents, and the decrease in gibberellin content indicate that PAs may promote carpospore release by regulating phytohormones. Transcriptome analysis revealed that after three days’ PAs treatment, the expression of photosynthesis- and antioxidant-related differentially expressed genes (DEGs) was increased. In addition, the MAPK signaling pathway and other pathways initiated by Ca²⁺ were activated, regulating the levels of ROS in G. lemaneiformis. The DEGs related to cell wall degradation and synthesis also indicated that PAs can regulate carpospore release. These findings confirm the role of PAs in promoting carpospore release, reveal the associated physiological changes and potentially involved signaling pathways, and provide new insights for further research and commercial application on G. lemaneiformis reproduction.

The diverse functions of arginine make it an indispensable component for overall cellular health and function. This study evaluated the effect and mechanism of arginine on autophagy, endoplasmic reticulum (ER) stress, and apoptosis, which are key pathways that regulate cell homeostasis and fate. The results showed that the imbalance of arginine (deficiency or excess) inhibited the growth of cells and disrupted cell homeostasis by increasing the level of autophagy, ER stress, as well as apoptosis. This in turn affects cell growth, homeostasis, and fate. Furthermore, the present study validated the lysosomal protein localization and arginine binding ability of the solute carrier family 38 member 9 (SLC38A9). This study also demonstrated SLC38A9 interaction with Ras-related GTP binding (Rag) complexes, the core sensor of amino acid signaling in the mechanistic target of rapamycin (mTOR) signaling pathway. This provides evidence for the sensing of arginine signals by SLC38A9. Furthermore, the siRNA-mediated knockdown of slc38a9 exacerbated the extent of the autophagy, ER stress, and apoptosis, while stable expression of SLC38A9 was found to alleviate these processes, as well as the disruption of cell homeostasis and function caused by arginine deficiency. The present study comprehensively explored the function of arginine in cell growth and fate, revealed the vital role and mechanism of SLC38A9 in arginine sensing, and expanded the understanding of the multiple functions of SLC38A9 in abalone.

Yeast nucleotides are known to modulate host immunity and gut microbiota. In teleosts, the intestinal mucosa represents a principal portal of viral entry, compromising barrier integrity, yet the mechanisms by which yeast nucleotides potentiate antiviral defenses remain to be elucidated. Herein, this study performed an eight-week feeding trial of coho salmon with graded yeast nucleotide levels (0, 125, 250, 500, and 1000 mg/kg), followed by intraperitoneal IHNV challenge with sampling at four days post-infection, and an in vitro assessment of intestinal mucus from the control and 500 mg/kg groups co-incubated with EPC cells and IHNV to evaluate antiviral efficacy. Coho salmon showed a biphasic growth response to dietary yeast nucleotides, with the 500 mg/kg group achieving the highest growth among all treatments. Yeast nucleotide enhanced intestinal tight junction integrity by upregulating proteins, such as Occludin, and potentiated mucosal immunity via modulation of NF-κB p65. Notably, yeast nucleotides reshaped gut microbiota and were associated with changes in lipid metabolism and increased levels of bioactive metabolites, with taxa such as Romboutsia, Bacillus, Turicibacter and Clostridium sensu stricto 1 showing significant correlations with these metabolic and immune parameters, although direct functional roles remain to be confirmed. Upon IHNV challenge, the 500 mg/kg group demonstrated significantly reduced cumulative mortality and ameliorated virus-induced disruption of intestinal barrier function compared to the control group. Finally, intestinal mucus from 500 mg/kg yeast nucleotides-fed fish conferred antiviral protection in vitro by upregulating host antiviral gene expression in EPC cells. These findings highlight dietary yeast nucleotides as key modulators of antiviral defense and intestinal barrier integrity potentially through microbiota-associated lipid metabolism and bioactive metabolite profiles, while acknowledging that further functional studies are required to establish causality, offering promising nutritional strategies against virus‐induced gut injury.

The glutamate–glutamine cycle is crucial for neuronal function; however, its role in pathological processes in teleost remains poorly understood. This study employed multi-omics approaches to investigate red-spotted grouper nervous necrosis virus (RGNNV)-induced neurodegeneration, integrating transcriptomic, proteomic, single-cell transcriptomic, and ATAC-seq analyses. Our findings revealed neuroactive ligand–receptor interaction and alanine–aspartate–glutamate metabolism as central pathways in RGNNV pathogenesis, particularly through dysregulation of ionotropic glutamate and gamma-aminobutyric acid (GABA) receptors. Significantly, we established a novel cell communication framework demonstrating that altered signaling within the glulb locus correlates with viral susceptibility. Glutamate accumulation led to dysregulation of glutathione and cysteine metabolism and subsequent p53-mediated ferroptosis, as evidenced by the activation of ferritin heavy polypeptide 1a (FTH1a), glutathione peroxidase 4a (GPX4a), and glutamate–cysteine ligase (GCLC) signals. In addition, RGNNV triggered ferroptosis through ferritinophagy-mediated Fenton reaction in grouper kidney cells. This study provides a robust framework for analyzing cell communication in non-model organisms and illuminates the critical role of glutamate–glutamine cycle dysregulation in RGNNV infection and neurodegeneration. Our findings offer new insights into the nervous necrosis virus pathogenesis in teleost and inform future therapeutic strategies.

This study contains integrated in situ observations from three research cruises (2019–2020), one of which encountered the tropical cyclone Sinlaku. The results show that the depth-integrated phytoplankton abundance and carbon biomass in the open sea was more than eightfold and sixfold, respectively, than those in the shelf. Diatoms were the major contributors in shelf areas. In the open sea, Trichodesmium was dominant, exhibiting abundances more than sixteen times higher than shelf areas and exceeding diatom and dinoflagellate abundances by three to nine orders of magnitude near the surface. In the period affected by tropical cyclone Sinlaku, total phytoplankton abundance and carbon biomass increased markedly compared to non-cyclone conditions, with horizontal and vertical distributions showing significant fluctuations due to the patchy distribution of high-density aggregations. Dinoflagellates were the dominant carbon biomass contributor at the 25 m layer, accounting for 71.13% of total carbon biomass. Species-level analysis of carbon biomass and equivalent spherical diameter confirmed that chain-forming diatoms and large-size dinoflagellates were significant participants in the carbon pool. Statistical and modeling approaches identified salinity and vertical stratification as key environmental drivers of shelf assemblages, while cyclone-induced coupling of temperature and nutrients played a critical role in shaping open-sea phytoplankton.

Oligotrophic bacteria with reduced genomes have relatively few transcriptional regulators and are thought to rely more than other bacteria on post-transcriptional regulation to respond to environmental stimuli. SAR11 bacteria are the most abundant group of heterotrophic bacteria in marine planktonic systems and are a model for understanding genome reduction in other free-living microorganisms. Here, we report a comprehensive, quantitative protein phosphorylation profile for SAR11 strain HTCC1062 grown under various environmentally relevant conditions, including light/dark cycles, temperature differences, and nutrient limitations, to investigate phosphorylation dynamics in this streamlined organism. Nearly half of proteins encoded by the genome were detected in phosphorylated forms under at least one condition. 1014 Ser/Thr/Tyr phosphorylation sites were observed in 1576 phosphopeptides from 555 phosphoproteins. Protein phosphorylation was concentrated in proteins for functions associated with nutrient acquisition and growth, such as ABC transporters, RNA polymerase, and ribosomal proteins. Prominent patterns in protein phosphorylation were detected across a range of culture conditions. In these cells, which previously have been shown to continuously express nearly their entire proteome, protein phosphorylation was more dynamic than protein abundance, supporting the hypothesis that post-transcriptional regulation by protein phosphorylation might play a large role in modulating protein activity. Our findings support a regulatory model characterized by minimal variation in protein expression but extensive protein phosphorylation. This model diverges from bacterial regulatory paradigms reliant on transcriptional control, and may be relevant to understanding other abundant heterotrophs with reduced genomes.