Hydrography is a key process modulating population structure, connectivity and redistribution of marine species, which is less concerned in Antarctic. The ocellated icefish, Chionodraco rastrospinosus, is among the most abundant fishes in the Antarctic. It contributes to the Southern Ocean ecosystem by linking producers with higher predators, but is vulnerable to climate change due to restricted distribution. The population structure remains poorly understood due to limited data and morphological similarities within Chionodraco. We analyzed mitochondrial COI and ND2 sequences of 133 C. rastrospinosus specimens from three Bransfield Strait areas (BS1, BS2, BS3), influenced by different water masses, to assess genetic diversity and population structure. C. rastrospinosus exhibited high haplotype and nucleotide diversity index (pi), with BS3 showing the lowest pi. Analysis of molecular variance revealed that variation among areas (COI: 99.42%; ND2: 96.78%) far exceeded within-population variation. The genetic differentiation coefficient (F-ST) indicated nonsignificant differences between BS1 and BS2, but values > 0.9 between BS3 and the others indicated strong divergence. Phylogenetic tree and haplotype network revealed two clusters, with BS1 and BS2 grouped together and BS3 forming a separate cluster. Integrating habitat suitability predictions with haplotype data further indicated strong connectivity between BS1 and BS2 but restricted linkage with BS3, reflecting contrasting hydrographic modulations of the Transitional Zonal Water with Weddell Sea influence and the Transitional Zonal Water with Bellingshausen influence. Overall, C. rastrospinosus in the BS exhibited high genetic diversity but diverged into two distinct geographic populations, highlighting hydrography and connectivity as key drivers of its population structure.

Ciliates constitute a vital component of eukaryotic diversity, playing an essential trophic role in aquatic ecosystems by mediating carbon and nutrient cycling. As specialized primary consumers in biofilms, cyrtophorian ciliates (Class Phyllopharyngea de Puytorac et al., 1974) are ubiquitous in periphytic habitats; yet, their biodiversity remains significantly underestimated compared to well-studied model groups. Here we document three species from the urban-adjacent coastal waters in East China. Integrative studies suggest that one of them represents a novel species and the other two are rare species. Morphological and molecular investigations were conducted on three species belonging to the order Dysteriida Deroux, 1976, Dysteria armata Huxley, 1857, Dysteria bella sp. nov., and Orthotrochilia agamalievi Deroux, 1976. For Dysteria armata (the type species of the genus), detailed morphometric data and an improved diagnosis are provided based on a Chinese population. The new species is characterized by size in vivo 75–110 × 40–60 μm, body long obovate, and seven right kineties including five frontoventral kineties. The SSU rRNA gene sequences were first obtained for all three species. Phylogenetic analyses reveal that Dysteria bella sp. nov. and D. armata form a fully supported sister clade. Consistent with morphological diversity, the molecular topology shows the non-monophyly of the genus Dysteria. Furthermore, the first molecular data for Orthotrochilia confirms its evolutionary distinctiveness from the genus Trochilioides. By providing detailed morphological and molecular characterizations of one new and two poorly known marine cyrtophorian species, this work not only advances our knowledge of the biodiversity within this specialized ciliate group but also resolves the systematic placement of the type species D. armata. Additionally, the acquisition of these sequences supplies essential genetic markers, filling critical gaps in molecular databases.

Coastal bays are critical land-sea interfaces increasingly threatened by anthropogenic activities, yet how pollution and trophic gradients shape microbial community assembly remains poorly understood. Here, we investigated spatial heterogeneity in environmental conditions and microbial community structure in surface (SW) and subsurface (SSW) waters of six bays along the Shandong Peninsula, China. Notably, diversity patterns did not follow a simple linear response to nutrient enrichment. While the eutrophic Rushan and Jinghai bays supported high biomass, the oligotrophic Rongcheng Bay exhibited high diversity and network complexity too. High-throughput sequencing of 18S and 16S rRNA genes revealed that microbial communities in surface and subsurface waters were shaped by distinct environmental drivers. While SW communities were primarily regulated by chemical nutrients (bottom-up), SSW communities were driven by physical factors and heavy metals, with Zn emerging as a key determinant for subsurface microeukaryotes. Co-occurrence network analysis further highlighted divergent interaction patterns, disturbed environment was dominated by positive correlations, indicating strong environmental filtering, whereas the stable Rongcheng Bay ecosystem featured a higher proportion of negative interactions. This suggests that niche differentiation and top-down control are critical for maintaining biodiversity and preventing competitive exclusion in oligotrophic waters. Our findings provide insights into how multiple pollution sources and environmental heterogeneity drive microbial assembly in coastal bays.

The toxicity of organophosphorus flame retardants (OPFRs) remains poorly understood, despite their widespread environmental presence and potential risks to human and ecological health. This study aimed to characterize the cardiovascular developmental toxicity of OPFRs using a high-throughput zebrafish screening model. Over thirty representative OPFRs, classified into three major groups-alkyl, aryl, and halogenated-were evaluated. Our results demonstrated that aryl-substituted OPFRs, such as triphenyl phosphate (TPHP) and tris(3,5-dimethylphenyl) phosphate (TXP), exhibit significantly more potent cardiotoxic effects compared to alkyl- and halogenated-substituted OPFRs. Specifically, heart rate of zebrafish increased by 8.3% and 11.9%, and cardiac output increased by 30.8% and 39.9% for TPHP and TXP, respectively, at a concentration of 160 μg/L. Additionally, exposure to aryl-substituted compounds like TPHP resulted in notable developmental abnormalities, including pericardial edema and skeletal bending. Molecular descriptor analysis further identified a series of essential structural features, including estrogen receptor agonist activity and bioconversion rates, which are closely linked to the observed cardiotoxicity, thus providing a mechanistic explanation for these effects. These findings offer valuable insights into the molecular mechanisms underlying OPFRs toxicity, which could inform the development of safer flame retardant alternatives. Moreover, addressing the research gaps in translating zebrafish findings to other species and real-world ecological scenarios should be further concerned.

As the most common ectoparasites on mackerel icefish (Champsocephalus gunnari Lönnberg 1905), which has great economic and ecological importance in the Southern Ocean, parasitic copepods and leeches can significantly affect fish health and survival and thus influence the sustainable use of this commercial fishery resource. Accurate identification of these parasites is essential for understanding their specific impacts on hosts and ecosystems, as well as for developing effective fisheries management. This study investigated 34 ectoparasites from 28 C. gunnari specimens at South Georgia in August 2023 using microscopy and mitochondrial cytochrome c oxidase I (CO I) markers. Morphological analysis tentatively identified 10 leeches as Notobdella nototheniae and 24 copepods as Eubrachiella antarctica. Microscopic examinations and morphological measurements revealed marked differences between male and female copepods. Additionally, CO I sequencing confirmed the leeches as N. nototheniae (98.81% similarity) but suggested the copepods were Parabrachiella merluccii (81.97-82.25% similarity). All sequences have been uploaded to Genbank. Maximum Likelihood phylogenetic trees were also constructed using the CO I sequence of both ectoparasites. The 10 leeches were identified as N. nototheniae, and the 24 copepods were E. antarctica in this study.

Ciliated protists (ciliates) represent a morphologically and genetically diverse group of single-celled eukaryotes, the phylogeny of which is critical for understanding eukaryotic evolution. Through international collaborations, the Laboratory of Protozoology at Ocean University of China (OUC-group) has conducted detailed research on ciliate phylogeny based on expanded taxonomic sampling, employing single gene as well as multi-gene markers, and phylogenomic datasets. We have systematically investigated > 1000 ciliate species spanning 40 orders, sampled from diverse biotopes including marine environments in China seas and freshwater wetlands. This comprehensive sampling has generated three key datasets: (1) genomic DNA extracts from 2600 strains, (2) 2300 sequences of marker genes, and (3) single-cell genomic and/or transcriptomic datasets from 120 species. Based on these datasets, the phylogenetic relationships covering all classes and most orders have been thoroughly reconstructed and investigated, resulting in the establishment of 93 new supraspecies taxa comprising two classes (Mesodiniea and Protocruziea), two subclasses (Protohypotrichia and Synhymenia), two orders (Wilbertomorphida and Lynnellida), 11 families, and 76 genera. Moreover, we have reconstructed a genome-scale tree of life for ciliates and provided an updated classification of the phylum Ciliophora. Furthermore, based on the robust phylogenetic tree of ciliates, we provide more reliable estimates for the origins and divergence times of the main ciliate groups. Future studies integrating advanced genomics, innovations in culturing and interdisciplinary applications will refine the ciliate tree of life, with broader impacts for our understanding of eukaryotic evolution and biodiversity.

Background: The Tibetan Plateau, which is known for its high elevation and low oxygen levels, presents a challenging environment for its inhabitants. To adapt to these hypoxic conditions, species of Schizothoracine, a subfamily of Cyprinidae, have developed unique physiological mechanisms and functions. Transforming growth factor-β (TGF-β) is a multifunctional cytokine involved in the regulation of cell growth, differentiation, apoptosis, and the cellular immune response. However, its specific role in adaptation to hypoxia remains poorly understood. Methods: In this study, we aimed to characterize the TGF-β1 gene in Gymnocypris dobula (Gd) and Schizothorax prenanti (Sp) and to test whether TGF-β1 contributes to hypoxia adaptation in plateau Schizothoracine fish. The predicted protein for Gd-TGF-β1 contains several primary domains, including cwf21 (cdc5 protein 21), GYF (Glycine-Tyrosine-Phenylalanine), FN1 (Fibronectin 1), a conservative domain, and a signal peptide. Results: The results of tissue distribution revealed that the mRNA level of TGF-β1 in brain, heart, muscle, skin, gills, and spleen—which are key tissues involved in oxygen sensing, transport, and physiological adaptation to hypoxic environments—was significantly lower in G. dobula than that in S. prenanti. Western blotting analysis revealed that the expression of activated TGF-β1 in G. dobula was significantly higher than that in S. prenanti. To investigate whether TGF-β1 in G. dobula possesses hypoxic adaptive features, Gd-TGF-β1 and Sp-TGF-β1 were cloned into an expression vector and transfected into 293-T cells, which are widely used due to their ease of culture, high transfectability, and well-characterized properties. We found that the survival rate of cells transfected with Gd-TGF-β1 was significantly higher than that of cells transfected with Sp-TGF-β1 after hypoxia treatment. Conclusions: These findings suggest that G. dobula may promote hypoxic adaptation through the activation and increased expression of TGF-β1. Changes in TGF-β1 expression may play a role in the adaptation of G. dobula to hypoxic conditions.

The northern Antarctic Peninsula (NAP), one of the fastest warming area around the Southern Ocean, hosts a large variety of endemic fish and is influenced by complex hydrography. However, the dynamics of fish diversity kept unclear and without monitoring. Monitoring of environmental DNA (eDNA) is a noninvasive, ecofriendly, and accurate approach for detecting aquatic organisms, including fish. In this study, the fish composition and diversity were detected by high-throughput sequencing of eDNA for the first time in the NAP. Overall, 32 species (1 order, 6 families, and 25 genera) of fishes were detected in the environmental water samples from 18 stations around the NAP, in which number of fish species were similar in the Drake Passage and the northern shelf of the South Shetland Islands (DP-SSIs) and the Bransfield Strait (BS). Most of the fish species were identified in previous Antarctic fish surveys using conventional methods, which supports the applicability of eDNA-based survey. Moreover, Pogonophryne albipinna was detected firstly in the NAP. Among the identified fish species, Champsocephalus gunnari and Notothenia rossii had the highest abundance (45.04% and 27.59%, respectively). There was difference in fish composition between the DP-SSIs and BS stations, although alpha diversity indices did not differ. The dissolved oxygen content and water temperature were the main drivers for the differences in fish species composition between areas. Our results indicated that eDNA could be a rapid and accurate biomonitoring approach for the entire Southern Ocean, particularly in areas with difficult logistics, in the future.

Two unusual algivorous ciliates, Paracoeloperix composita gen. nov., sp. nov. and Chlamydonella wangi sp. nov., were collected from marine habitats in China. Their morphology and molecular phylogeny were investigated using microscopical and ribosomal gene sequencing techniques. Paracoeloperix gen. nov. can be distinguished from its most closely related genus, Coeloperix, by its distinct trilinear oral ciliature and its small subunit ribosomal ribonucleic acid (SSU rRNA) gene sequence divergence. Paracoeloperix composita gen. nov., sp. nov. is characterized by having trilinear perioral kineties, a complete cross-striated band, finger-like tentacles on the ventral side, and anterior and left terminal fragments. Chlamydonella wangi sp. nov. differs from its congeners by having a reniform body, four or five contractile vacuoles, 17–19 somatic kineties, and 2.6%–8.3% SSU rDNA sequence dissimilarity. The systematic placements of the family Lynchellidae and the genus Paracoeloperix gen. nov. remain elusive owing to their low support values in phylogenetic trees and the unstable topology of these trees. Furthermore, the present study rejects the monophyly of the genus Chlamydonella because Chlamydonella wangi sp. nov. is closely related to Chlamydonellopsis calkinsi. Additionally, an illustrated identification key of Lynchellidae genera and a conjecture based on mapping between morphological features and the SSU rDNA tree are provided.

A study was conducted to evaluate the effect of enzymatic hydrolysis of sargassum mixed with fish protein hydrolysis product (named "SFPH" in the present study) as a substitute for fish meal in shrimp feed. Six isonitrogenous and isolipidic diets (SFPH was used to replace 0 %, 5 %, 10 %, 20 %, 30 % and 40 % of fish meal protein) were administered to Litopenaeus vannamei (initial body weight: 0.9 g) for 8 weeks. Results showed that SFPH can replace 30 % of fish meal without affecting the growth performance of shrimp. However, 40 % of SFPH substitution significantly inhibited the weight gain rate (WGR) and specific growth rate (SGR) of shrimp. SFPH substitution had little effect on the composition of fatty acids, but SFPH substitution significantly reduced the contents of histidine, phenylalanine, tyrosine and taurine in the whole shrimp body. SFPH improved the structure of shrimp hepatopancreas and muscle when no more than 20 % of the fish meal was replaced. However, 40 %SFPH substitution significantly disrupted the structure of hepatopancreas and muscle. SFPH substitution significantly affected the antioxidant capacity, as manifested by a gradual decrease in T-AOC activity. With respect to endoplasmic reticulum stress, 30 %SFPH and 40 %SFPH groups significantly increased the mRNA expression of eif2 alpha and hip. In summary, SFPH can replace 30 % of fish meal protein in shrimp feed without affecting shrimp growth. However, when SFPH exceeds 30 %, it can easily induce oxidative stress and endoplasmic reticulum stress in the hepatopancreas.

The common squid, Todarodes pacificus, is an important commercial species that inhabits the northwest Pacific Ocean, particularly the East Japan Sea, the Pacific coast of Japan, and the East China Sea. In this study, we chose 29 individuals from three areas: one type from the Sea of Japan and two types from the East China Sea. A total of 43,529 SNPs were obtained using genotyping-by-sequencing (GBS). Our analyses revealed low genetic diversity and genetic differentiation in each type. Heterozygote deficiency and inbreeding have caused this low level of genetic diversity. Population structure analysis indicated that the three types were genetically similar, which may be attributed to strong gene flow combined with the demographic history events during the last 2 million years. This new GBS application technique provides valuable information for the conservation of marine species genetics and could be useful for the effective management of this resource.

Seed hardness is an important quality trait of vegetable soybean. To determine the factors underlying seed hardness, two landraces with contrasting seed hardness, Niumaohuang (low seed hardness) and Pixiansilicao (high seed hardness), were selected from 216 soybean accessions originating from 26 provinces in China. The contents of the main components in vegetable soybean seeds such as water, soluble sugar, starch, protein and oil were measured, and transcriptome analyses performed during five stages of seed developmental. Transcriptome analysis indicates that during the middle and late stages of seed development, a large number of genes involved in the synthesis or degradation of starch, storage protein, and fatty acids were differentially expressed, leading to differences in the accumulation of stored substances during seed maturation among Niumaohuang and Pixiansilicao. The activity of cell proliferation and the formation of cell walls in the middle and late stages of seed development may also affect the hardness of seeds to a certain extent. In addition, weighted gene co-expression network analysis (WGCNA) was undertaken to identify co-expressed gene modules and hub genes that regulate seed hardness. Overexpression of a candidate seed hardness regulatory hub gene, GmSWEET2, resulted in increased seed hardness. In this study, the important role of GmSWEET2 in regulating the hardness of vegetable soybean seeds was verified and numerous potential key regulators controlling seed hardness and the proportion of seed components were identified, laying the groundwork for improving the texture of vegetable soybean.

The Japanese anchovy, Engraulis japonicus , is an important economic fish that is distributed in the northwest Pacific Ocean. The effective assessment and management of the Engraulis japonicus fishery requires reliable information regarding its population’s genetic structure. The recent development of double digest restriction-site associated DNA sequencing (ddRAD-Seq) methods may contribute to the discovery of SNPs and the assessment of genetic structure. In our study, 98 single nucleotide polymorphism (SNP) markers were developed using ddRAD-Seq. The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.3333 to 0.8000 and 0.2778 to 0.5000, respectively. The polymorphism information content (PIC) ranged from 0.239198 to 0.375. All loci have been substantiated to follow the Hardy–Weinberg equilibrium. These novel polymorphic SNP markers will play an important role in the genetic research of E.japonicus , which will be beneficial to the development and utilization of E.japonicus resources. This study aims to provide technical support for the research of genetic diversity of E. japonicus populations through the development of SNP markers.

Prostomatean ciliates inhabit a wide range of aquatic environments and serve as a trophic link in food webs. However, the biodiversity and molecular phylogeny of the Prostomatea, especially the order Prostomatida, is poorly known owing to undersampling and the paucity of molecular data. Here, three prostomatid ciliates, Platina marina gen. nov., sp. nov., Parametacystis pulchra gen. nov., sp. nov. and Apsiktrata gracilis, were studied based on morphological data and small subunit ribosomal ribonucleic acid (SSU rRNA) gene sequences. The two new genera show a close relationship with the class Plagiopylea but a distant relationship with Metacystis, which bears a strong morphological similarity to the two new genera. The simplified oral ciliature can be regarded as a synapomorphy of the two new genera. The SSU rRNA gene of a representative of the family Apsiktratidae was sequenced for the first time. Morphological and phylogenetic analyses suggest that Apsiktratidae might be more closely related to Prorodontida than to Prostomatida, and the oral basket might be more phylogenetically informative than the brosse in distinguishing Prorodontida and Prostomatida. Supplementation with rare taxa reveals a close association between the Prostomatida and Trimyemidae. The putative secondary structure of the SSU rRNA V9 region suggests a sister relationship between the order Prostomatida and the class Plagiopylea.

Soybean production is significantly impacted by Phytophthora root rot (PRR), which is caused by Phytophthora sojae. The nucleotide-binding leucine-rich repeat (NLR) gene family plays a crucial role in plant disease resistance. However, current understanding of the function of soybean NLR genes in resistance to PRR is limited. To address this knowledge gap, transgenic soybean plants overexpressing the NLR gene (Glyma.18g283200) were generated to elucidate the molecular mechanism of resistance. Here, transcript changes and metabolic differences were investigated at three time points (12, 24, and 36 h) after P. sojae infection in hypocotyls of two soybean lines, Dongnong 50 (susceptible line, WT) and Glyma.18g283200 overexpression line (resistant line, OE). Based on the changes in differentially expressed genes (DEGs) in response to P. sojae infection in different lines and at different time points, it was speculated that HOPZ-ACTIVATED RESISTANCE 1 (ZAR1), valine, leucine, and isoleucine degradation, and phytohormone signaling may be involved in the defense response of soybean to P. sojae at the transcriptome level by GO term and KEGG pathway enrichment analysis. Differentially accumulated metabolites (DAMs) analysis revealed that a total of 223 and 210 differential metabolites were identified in the positive ion (POS) and negative ion (NEG) modes, respectively. An integrated pathway-level analysis of transcriptomics (obtained by RNA-seq) and metabolomics data revealed that isoflavone biosynthesis was associated with disease resistance. This work provides valuable insights that can be used in breeding programs aiming to enhance soybean resistance against PRR.

Despite advancements in high-resolution screening techniques, the identification of novel perfluoroalkyl and polyfluoroalkyl substances (PFAS) remains challenging without prior structural information. In view of this, we proposed and implemented a new data-driven algorithm to calculate spectral similarity among PFAS, facilitating the generation of molecular networks to screen for unknown compounds. Using this approach, 81 PFAS across 12 distinct classes were identified in soil samples collected near an industrial park in Shandong Province, China, including the first reported occurrence of 12 iodine-substituted PFAS. Among them, the standards of four iodine-substituted polyfluorinated ether sulfonates (I-PFESA) were successfully synthesized, enabling structural confirmation and subsequent quantitative analysis. Although the median concentration of ∑I-PFESA (0.74 ng/g dw) in soil samples was lower than that of ∑H-PFESA (hydrogen-substituted, 61.96 ng/g dw) and ∑Cl-PFESA (chlorine-substituted, 2.98 ng/g dw), embryotoxicity assays in zebrafish revealed that 6:2 I-PFESA exhibited greater toxicity compared to 6:2 Cl-PFESA of the same chain length. This highlights the need for a closer examination of the toxic effects of I-PFESA. Notably, the proposed algorithm, based on novel PFAS spectral similarity, provides new perspectives on the environmental behavior and transformation of I-PFESA, although further investigation is required to elucidate the underlying mechanisms of their toxicity.

It has long been recognized that ciliates play a crucial role in microbial food webs in all kinds of biotopes. However, basic information about their species diversity, geographic distribution, and ecological function is scant, and molecular data are unavailable for most species. As a new contribution, a comprehensive survey of the diversity of ciliates in the Lake Weishan freshwater Wetland in northern China has recently been undertaken. In the present study, four species of the subclass Cyrtophoria were morphologically investigated including a new one, Phascolodon paravorticella sp. nov., which is characterized by having a body size 40-55 x 25-40 mu m, 4 or 5 right and 4-7 left kineties, 20-22 nematodesmal rods, and two diagonally positioned contractile vacuoles. Three known forms, namely Gastronauta aloisi, Trithigmostoma cucullulus, and Trithigmostoma steini, are re-described based on the Lake Weishan Wetland populations. Additionally, phylogenetic analyses based on 18S rRNA gene sequences support the validity of the family Gastronautidae and imply that Trithigmostoma cucullulus contains cryptic species. The phylogenetic relationship between the families Chilodonellidae and Gastronautidae remains uncertain.

The subclass Cyrtophoria is a group of morphologically specialized ciliates with diverse characteristics, which can be found in a variety of aquatic and terrestrial habitats. In the present study, two cyrtophorian ciliates, Aegyria oliva Claparede & Lachmann, 1859 and A. peculiaris sp. nov., isolated from coastal waters of China, were investigated based on microscopic observations of live and protargol-stained specimens, and SSU rRNA gene sequence analyses. For A. oliva, the type species of the genus, detailed morphometric data, and improved diagnosis are provided. The new species, Aegyria peculiaris sp. nov. is characterized by a body size of 70-115 x 30-65 mu m in vivo, an inverted oval body shape with a protrusion at the anterior left and a posterior bulge on the dorsal side, 45-58 somatic kineties, 31-46 nematodesmal rods, 4-6 transpodial segments, and about six contractile vacuoles. Phylogenetic analyses unveiled a close relationship between the newly identified species and A. foissneri, thereby confirming the monophyly of the genus Aegyria.http://zoobank.org/urn:lsid:zoobank.org:pub:F5566374-DA6C-4E95-B8DA-19F935D949C8