Ecological Risks of Zinc Oxide Nanoparticles for Early Life Stages of Obscure Puffer (Takifugu obscurus).

Nanoparticles of zinc oxide (ZnO NPs) are extensively used in various applications, and their widespread use leads to their environmental presence, particularly in wastewater treatment plant effluents, rivers, and soil. This study focuses on the obscure puffer, Takifugu obscurus, an economically important fish in China, aiming to assess the toxic effects of ZnO NPs on its early life stages, emphasizing the need for understanding the ecological implications of ZnO NP exposure in aquatic environments. Exposure during the hatching stage resulted in a significant decrease in hatching rates, with embryos displaying surface coating at higher ZnO NP concentrations. Newly hatched larvae experienced deformities, and post-hatching exposure led to pronounced reductions in survival rates, particularly with higher ZnO NP concentrations. Two-month-old juveniles exposed to increasing ZnO NP concentrations exhibited a consistent decline in survival rates, emphasizing concentration-dependent adverse effects. Biochemical analyses revealed elevated malondialdehyde (MDA) levels and decreased glutathione (GSH), superoxide dismutase (SOD), and catalase (CAT) activities in various tissues, indicating oxidative stress. This study underscores the ecological risks of ZnO NP contamination in aquatic environments, emphasizing the need for careful consideration of nanoparticle exposure in aquatic ecosystems.

The effects of a polystyrene nanoplastic on the immune response and gut microbiota of Eriocheir sinensis and its post-recovery state.

Although there is increasing concern about the toxicity of nanoplastics, the effects of nanoplastic exposure and subsequent recovery on immune responses, as well as antioxidant responses and gut microbiota, in crustaceans are rarely reported. In this study, the nonspecific immunity and antioxidant defense of Eriocheir sinensis were evaluated after acute exposure to various concentrations (0, 2.5, 5, 10 and 20 mg/L) of 75-nm polystyrene nanoplastics (PS-NPs) for 48 h, as well as after 7 days of recovery from the nanoplastic environment. The results showed that, after 48 h of exposure, nanoplastics were observed in the gills, hepatopancreas and gut. However, no nanoplastics were found in the gut after 7 days of recovery. Under nanoplastic-induced stress, Hc, Relish, proPO, and LITAF mRNA levels increased in the gills and hepatopancreas for 48 h. Expression of the myd88, Hc, Relish and proPO genes decreased in the gills during the 7-day recovery period. Exposure to nanoplastics for 48 h and recovery for 7 days significantly decreased the activities of lysozyme (LZM) alkaline phosphatase (AKP), total superoxide dismutase (SOD) and phenoloxidase (POD) and, glutathione peroxidase (GPX) in the hepatopancreas. Meanwhile, the relative abundance of pathogens exposed to 10 mg/L nanoplastics for 48 h increased at the species level, and these pathogens decreased significantly in the 7-day recovery period. These results suggested that exposure to nanoplastics for 48 h affected the activities of immune system enzymes and expression of immune-related genes in Eriocheir sinensis and altered the diversity and composition of their gut microbiota. E. sinensis could not recover from damage to the hepatopancreas within a 7-day recovery period. The results of this study provided insight into the effects of nanoplastics on crustaceans and it filled a gap in research on crustacean recovery after exposure to nanoplastics.

Complete mitochondrial genome and phylogenetic analysis of Sineleotris saccharae (Perciformes, Odontobutiae).

The freshwater sleeper, Sineleotris saccharae Herre, 1940 is a member of the Odontobutiae family, widely distributed in southern China. In the present study, we determined the complete mitochondrial genome of S. saccharae for the first time and analyzed its evolutionary relationship. The complete mitochondrial genome of S. saccharae was 16,487 bp long, and had 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNA (rRNAs) and a control region (CR). The mitogenome of S. saccharae shared the same gene organization and orientation as other teleosts. According to phylogenetic research, S. saccharae was sister to S. chalmersi with high support value, providing the monophyly of the genus Sineleotris. These results will be helpful for understanding the systematics of the odontobutids.

Fern Spores-"Ready-to-Use" Standards for Plant Genome Size Estimation Using a Flow Cytometric Approach.

Spores and pollen of plants were used as flow cytometric materials to efficiently infer genome sizes. Given this advantage, they hold great potential for various flow cytometric applications, particularly as plant genome size standards. To develop such novel standards, we investigated conditions of pretreatment (bead vortex), buffer, and reliable genome sizes of three fern spore collections-Cibotium taiwanense "Kuo4395", Sphaeropteris lepifera "Tang0001", and Alsophila metteniana "Lee s.n.". Additionally, up to 30 year-old spore collections were obtained from herbarium specimens and from samples stored at 4 °C; their spore nuclei were extracted, and the quality and quantity of these nucleus extractions through storage ages were examined. Nuclear extractions with a longer bead vortex duration or lower spore/bead ratio generally resulted in a higher recovered quantity but a lower quality or purity. For each spore standard, the protocol optimization was determined by their performance in bead vortex conditions, and a 1C genome size was further inferred by linear regression (C. taiwanense "Kuo4395" = 5.058 pg; S. lepifera "Tang0001" = 7.117 pg; and A. metteniana "Lee s.n." = 19.379 pg). Spore nucleus quality and quantity are significantly negatively correlated with storage ages. Nuclear extractions of 10-year-old refrigerated spores remained qualified as a genome size standard; however, none of the herbarium spore collections fit such criteria. Our study is the first to develop and apply dried and refrigerated spores for genome size standards. These standards are ready to use, easy to manipulate, and feature long-term storage in comparison with traditionally used standards of fresh leaves.

Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea).

The Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

The complete mitogenome of freshwater gammarid Grandidierella taihuensis (Crustacea: Amphipoda).

The freshwater gammarid Grandidierella taihuensis is an important composition of benthic community. In this study, the complete mitogenome sequences of G. taihuensis are determined using next-generation and PacBio long-read sequencing. The mitogenome of G. taihuensis is 15,099 bp in size, and consisted of 13 protein-coding genes, two ribosomal RNA genes, 22 tRNA genes, and a putative control region. Gene arrangement is as same as that of G. rubroantennata. The base composition of the entire mitogenome showed a conspicuous A + T bias of 69.4%. The mitogenome data produced in this study provides a useful resource for future evolutionary and ecological studies.

The complete mitochondrial genome of Callionymus olidus (Perciformes Callionymidae).

In this study, we present the complete mitogenome and a phylogenetic analysis of Callionymus olidus, determined by long PCR and primer walking methods. The complete mitochondrial genome is a circular molecule of 16,491 bp in length and contains the same set of 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA)), and a control region as other bony fishes. The base composition of the entire mitogenome showed a slight excess of AT bias. The entire mitogenome data produced in this study provides the genomic resources available for future evolutionary studies.

Transcriptional response provides insights into the effect of chronic polystyrene nanoplastic exposure on Daphnia pulex.

Nanoplastic pollution is widespread and persistent across global water systems and can cause a negative effect on aquatic organisms, especially the zooplankter which is the keystone of the food chain. The present study uses RNA sequencing to assess the global change in gene expression caused by 21 days of exposure to 75 nm polystyrene (PS) nanoplastics on Daphnia pulex, a model organism for ecotoxicity. With the threshold value at P value < 0.05 and fold change >2, 244 differentially expressed genes were obtained. Combined with real-time PCR validation of several selected genes, our results indicated that a distinct expression profile of key genes, including downregulated trehalose transporter, trehalose 6-phosphate synthase/phosphatase, chitinase and cathepsin-L as well as upregulated doublesex 1 and doublesex and mab-3 related transcription factor-like protein, contributed to the toxic effects of chronic nanoplastic exposure on Daphnia, such as slowed growth, subdued reproductive ability and reproductive pattern shifting. Our study also showed that chronic exposure to nanoplastic changed the sex ratio of D. pulex neonates. By integrating the gene expression pattern in an important model organism, this study gained insight into the molecular mechanisms of the toxic effect of chronic PS nanoplastic exposure on D. pulex, which may also extend to other nanoplastics or aquatic animals.

Correlation between antibiotic-induced feeding depression and body size reduction in zooplankton (rotifer, Brachionus calyciflorus): Neural response and digestive enzyme inhibition.

The study analyzed the correlation between the antibiotic-induced feeding depression and body size reduction in rotifer, Brachionus calyciflorus, involving exposure, post-exposure and re-exposure periods. The filtration and ingestion rates of the rotifers were inhibited in these three exposure periods at any given concentration of the antibiotic sulfamethazine (SMZ). As food for rotifer, the cell size of the green algae was unchanged, which indicated that it could not drive feeding depression. Secondly, several corresponding physiological responses were considered. Reactive oxygen species (ROS) levels increased in the post-exposure and the re-exposure; acetylcholinesterase (AChE) activity was significantly decreased in the exposure and the re-exposure, whereas it was induced in the post-exposure. The activities of amylase and lipase were always inhibited in these three exposure periods. Additionally, significant decreases in lorica length, width and biovolume of rotifers occurred after the feeding depression. Statistical analysis indicated a positive correlation between the activity of the digestive enzyme and the body size. Our results demonstrated that SMZ could influence the neurotransmission, inhibit the activity of the digestive enzyme, and finally result in body size reduction. These results provided an integrated perspective on assessing the toxicity effects of antibiotic in non-lethal dosage on the feeding behavior of non-target aquatic organisms.

Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes.

Naturally derived toxins from animals are good raw materials for drug development. As a representative venomous teleost, Chinese yellow catfish (Pelteobagrus fulvidraco) can provide valuable resources for studies on toxin genes. Its venom glands are located in the pectoral and dorsal fins. Although with such interesting biologic traits and great value in economy, Chinese yellow catfish is still lacking a sequenced genome. Here, we report a high-quality genome assembly of Chinese yellow catfish using a combination of next-generation Illumina and third-generation PacBio sequencing platforms. The final assembly reached 714 Mb, with a contig N50 of 970 kb and a scaffold N50 of 3.65 Mb, respectively. We also annotated 21,562 protein-coding genes, in which 97.59% were assigned at least one functional annotation. Based on the genome sequence, we analyzed toxin genes in Chinese yellow catfish. Finally, we identified 207 toxin genes and classified them into three major groups. Interestingly, we also expanded a previously reported sex-related region (to ≈6 Mb) in the achieved genome assembly, and localized two important toxin genes within this region. In summary, we assembled a high-quality genome of Chinese yellow catfish and performed high-throughput identification of toxin genes from a genomic view. Therefore, the limited number of toxin sequences in public databases will be remarkably improved once we integrate multi-omics data from more and more sequenced species.

Complete mitochondrial genome of freshwater goby Rhinogobius cliffordpopei (Perciformes, Gobiidae): genome characterization and phylogenetic analysis.

Freshwater gobies Rhinogobius cliffordpopei and R. giurinus are invasive species with particular concern because they have become dominant and were fierce competitors in the invaded areas in Yunnan-Guizhou Plateau (southwest of China). Information about genetic characteristics of R. giurinus have been published, but there were still no relevant reports about R. cliffordpopei. In present study, the complete mitochondrial genome of R. cliffordpopei was determined, which was 16,511 bp in length with A + T content of 51.1%, consisting of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the R. cliffordpopei complete mtDNA were identical to most of other teleosts. Phylogenetic analyses placed R. cliffordpopei in a well-supported monophyletic cluster with other Rhinogobius fish. But the phylogenetic relationship between genus Rhinogobius and Tridentiger remained to be resolved.

Complete mitochondrial genome of Odontobutis haifengensis (Perciformes, Odontobutiae): A unique rearrangement of tRNAs and additional non-coding regions identified in the genus Odontobutis.

Herein, the complete mitochondrial genome of Odontobutis haifengensis was sequenced for the first time. The O. haifengensis mitogenome was 17,016bp in length and included 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (CR). The genome organization, base composition, codon usage, and gene rearrangement was similar to other Odontobutis species. Furthermore, a tRNA gene rearrangement within the SLH cluster was found to be identical to other Odontobutis species. Moreover, the gene order and the positions of additional intergenic non-coding regions suggests that the observed unique gene rearrangement resulted from a tandem duplication and random loss of large-scale gene regions. Additionally, phylogenetic analysis showed that Odontobutis species form a monophyletic clade due to the conserved mitochondrial gene rearrangement. This study provides useful information that aids in a better understanding of mitogenomic diversity and evolutionary patterns of Odontobutidae species.

Single and mixture toxicities of BDE-47, 6-OH-BDE-47 and 6-MeO-BDE-47 on the feeding activity of Daphnia magna: From behavior assessment to neurotoxicity.

Although 2,2',4,4'-tetrabrominated diphenyl ether (BDE-47), 6-hydroxy-2,2',4,4'-tetrabromodiphenyl ether (6-OH-BDE-47) and 6-methoxy-2,2',4,4'-tetrabromodiphenyl ether (6-MeO-BDE-47) clearly disrupt the endocrine system, current knowledge of their single and/or mixture toxicities on other behaviors of aquatic organisms remains limited. In the present study, Daphnia magna was used to investigate the single and mixture toxicities of BDE-47, 6-OH-BDE-47 and 6-MeO-BDE-47 as measured by inhibition of feeding during exposure and post-exposure periods. Additionally, the biochemical performance, i.e., the activities of super oxidase dismutase (SOD), glutathione peroxidase (GPx) and acetylcholinesterase (AChE) of the test organism was studied to investigate the potential mechanisms of the toxicity of the target compounds. The three target compounds produced an obvious depressive effect on feeding behavior during the exposure period, and the effect increased with increasing concentrations. D. magna was most sensitive to 6-OH-BDE-47. The toxicity of the ternary mixture showed an obvious concentration-dependent effect, whereas the binary mixture toxicity showed the characteristics of hormesis. During the post-exposure period, overcompensation occurred, indicating a short-term effect of the target compounds on D. magna. Additionally, significant changes occurred in neurological responses, indicating that these compounds might have neurobehavioral toxicity in D. magna. The decrease in oxidative stress enzymes (SOD and GPx) indicated that the antioxidant response of D. magna was destroyed.

[Abundance of Toxic and Non-toxic Microcystis sp. in Lake Hongze and Its Correlation with Environmental Factors].

In the present study, the eutrophic level of 30 water samples collected from Lake hongze in August 2014 were analyzed, and the abundance of toxic and non-toxic Microcystis sp., together with their spatial distribution, was investigated by quantitative real-time PCR techniques. The results showed that the average concentrations of total nitrogen and total phosphorus were 1.63 and 0.11 mg x L(-1), respectively. The trophic state index ( TSI) ranged from 58.1 to 73.6, and the water quality was in the state of eutrophication based on TSI. Toxic Microcystis was widely distributed in Lake Hongze, and its abundance varied sharply, from 1. 13 x 10(4) to 3.51 x 10(6) copies x mL(-1), and the abundance of total Microcystis ranged from 1.06 x 10(5) to 1.10 x 10(7) copies x m(-1), meanwhile, the proportion of toxic Microcystis in the total Microcystis ranged from 8.5% to 38.5%, with the average value of 23.6%. Correlation analysis indicated that there was a significant positive correlation among total Mirocystis, toxic Microcystis and the toxic proportion (P < 0.01). The abundance of total and toxic Microcystis was significantly positively correlated to chlorophyll a ( Chl-a) concentrations and TSI (P < 0.01), but was negatively correlated to transparency (SD) (P < 0.01). The ratio of toxic Microcystis to total Microcystis was significantly positively correlated to Chl-a, TN, TP and TSI (P < 0.01), but significantly negatively correlated to the ratio of TN to TP and SD (P < 0.01). Therefore, reducing total nitrogen and phosphorus concentrations could not only lower the eutrophication level of Lake Hongze, but also inhibit the competition advantage of the toxic Microcystis over non-toxic Microcystis.

Complete mitochondrial genome of Chinese icefish Neosalanx tangkahkeiis (Salmoniformes, Salangidae): comparison reveals Neosalanx taihuensis not a valid name.

The complete mitochondrial genome of Neosalanx tangkahkeiis was determined to be 16,550 bp in length with (A+T) content of 49.7%, and it consists of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the N. tangkahkeiis complete mtDNA were identical to most of other vertebrates. The sequence comparison showed that mitogenome of N. tangkahkeiis had a 99.9% of similarity with so-called N. taihuensis, indicating they are the same species and N. taihuensis is not a valid name.

The dynamics of toxic and nontoxic Microcystis during bloom in the large shallow lake, Lake Taihu, China.

Lake Taihu is a large shallow freshwater lake (surface area 2,338 km(2), mean depth 1.9 m) in China, which has experienced toxic cyanobacterial bloom dominated by Microcystis annually during the last few decades. In the present study, the dynamics of toxic and nontoxic Microcystis in three sampling stations (Meiliang Bay (site N2), Gonghu Bay (site N4), and the lake center area (site S4)) were quantified using quantitative real-time PCR (qPCR) during bloom periods from April to September, 2010. Our data showed that the abundance of toxic Microcystis and the toxic proportion gradually increased from April to August in water samples and reached the peak in August. During the study period, toxic Microcystis genotypes comprised between 26.2 and 64.3, between 4.4 and 22.1, and between 10.4 and 20.6 % of the total Microcystis populations in the three sampling sites, respectively. Correlation analysis suggested that there was a strong positive relationship between total Microcystis, toxic Microcystis and the toxic proportion. Chlorophyll a, total phosphorus, and water temperature were positively correlated with the abundances of total Microcystis and toxic Microcystis. Furthermore, the toxic proportion was positively correlated with total phosphorus (P < 0.05) and water temperature (P < 0.01), showing that global warming together with eutrophication could promote more frequent toxic blooms.