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Gill and brain transcriptomic analysis of mandarin fish(Siniperca chuatsi) reveals hypoxia-induced mitochondrial dysfunction and modulation of metabolism

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COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2025年 53卷 101367页

作者： Ding, Weidong Cao, Liping Cao, Zheming bing, xuwen Chinese Acad Fishery Sci Minist Agr Freshwater Fisheries Res Ctr Key Lab Freshwater Fisheries & Germplasm Resources Wuxi 214081 Peoples R China

The oxygen content in the fish ponds is facing greater challenges than before in the aquaculture of mandarin fish (Siniperca chuatsi) due to the change of climate and eutrophication. Until now, little is known about the molecular mechanisms underlying the harmful effects of hypoxia on this species. In this work, we built transcriptomes for the mandarin fish that were exposed to decreased oxygen concentration at two times points (24 hand 96 h). The respiratory metabolism activities of pyruvate kinase (PK), hexokinase (HK), lactate dehydrogenase (LDH), succinate dehydrogenase (SDH) and malate dehydrogenase (MDH) had different significantly changes during hypoxic treatment. Histological observation of the gill and brain also revealed some damages by hypoxia. A total of 196,355 transcripts were involved in the Gene Ontology analysis, and the numbers of differentially expressed genes (DEGs) in the brain and the gill between the control and experiment groups are 141 and 552 respectively involved in the different hypoxic stress time. The DEGs were then analyzed using KEGG enrichment analysis. The results showed significant differences in the expression of some genes involved in ribosome pathways,biosynthesis of amino acids, hippo signaling pathway, and pentose phosphate pathway,glycolysis/gluconeogenesis pathway and the TCA cycle. The huge number of transcriptome sequences collected in this study has enhanced the mandarin fish gene resources, and the identified DEGs and related pathway analysis give essential information for understanding biological responses to hypoxia.

关键词： Mandarin fish Transcriptome Hypoxia DEGs

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Transcriptomic responses of the liver of mandarin fish (Siniperca chuatsi) under hypoxic stress

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JOURNAL OF FISH BIOLOGY 2023年第1期103卷 44-58页

作者： Ding, Weidong Cao, Liping Cao, Zheming bing, xuwen Chinese Acad Fishery Sci Freshwater Fisheries Res Ctr Key Lab Freshwater Fisheries & Germplasm Resources Minist Agr Wuxi 214081 Peoples R China

Environmental hypoxia is becoming more prevalent in aquatic environments of mandarin fish (Siniperca chuatsi) aquaculture because of eutrophication and climate change. Little information is available on the molecular mechanisms of the detrimental effects of hypoxia in this species. In this study, the authors assembled a transcriptome for mandarin fish exposed to lower oxygen conditions at different times (24 and 96 h). The antioxidant enzymatic activities of catalase, glutathione, superoxide dismutase, glutamic pyruvic transaminase and malondialdehyde significantly increased at 6 or 12 h but decreased after reaching a climax during 96 h hypoxia stress. The gene ontology study revealed 27,616 transcripts, whereas the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed 25 linked pathways. Significant changes in the expression of certain genes involved in protein processing in the endoplasmic reticulum, the calcium signalling system and inositol phosphate metabolism were discovered using the KEGG pathway analysis. In the liver, 97 genes were differentially expressed between the control and experimental groups. The expression level of 28 differentially expressed genes (DEGs) under different hypoxic stress conditions was detected using real-time PCR and compared to transcriptome sequencing results. The result showed that some genes in the experimental group associated with hypoxic stress, such as hif, ho-1a, ho-1b, igfbp1, hsp90 alpha and hsp90 beta, were significantly upregulated compared with those in the control group. The large amount of transcriptome data from this research has enlarged the mandarin fish gene and genome bioinformation. The identified DEGs and pathways are useful in further studies of biological responses to hypoxia.

关键词： differentially expressed genes hypoxia mandarin fish transcriptome

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Paeonol increases the antioxidant and anti-inflammatory capacity of gibel carp (Carassius auratus gibelio) challenged with Aeromonas hydrophila

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FISH & SHELLFISH IMMUNOLOGY 2022年第0期123卷 479-488页

作者： Gu, Yipeng Chen, Kai Xi, bingwen Xie, Jun bing, xuwen Nanjing Agr Univ Wuxi Fisheries Coll Wuxi 214081 Peoples R China Chinese Acad Fishery Sci Freshwater Fisheries Res Ctr Key Lab Freshwater Fisheries & Germplasm Resources Minist Agr Wuxi 214081 Peoples R China

Paeonol, a naturally occurring polyphenol isolated from medical plant, has been known to exhibit anti-oxidative and anti-inflammatory effects. In order to evaluate the effect of paeonol on Carassius auratus gibelio infected by pathogenic bacteria Aeromonas hydriphila. 750 fish were randomly divided into 5 groups, which separately treated with 0.85% sterile saline (blank), A. hydriphila (negative control), A. hydriphila with paeonol (4 mg/kg, 64 mg/kg), and A. hydriphila with enrofloxacin (12 mg/kg, positive control). Fish were anaesthetized with MS -222 (100 mg/L), and samples were collected at 6 and 72 h after A. hydriphila challenge. The results showed that compared with the negative group, the survival in paeonol groups marked increased by 14.75% and 18.94%. The plasma immunoglobulin M (IgM) was notably increased, and low density lipoprotein (LDL) was significantly decreased in paeonol groups at 6 h (P < 0.05). The antioxidative enzymes catalase (CAT), total antioxidant capacity (T-AOC) and glutathione peroxidase (GSH-Px) were significantly increased in paeonol groups at 6 h, while malondialdehyde (MDA) and myeloperoxidase (MPO) contents were lower (P < 0.05). The inflammatory related genes MyD88 and TLR-5 were significantly downregulated, and the TLR-3 was significantly increased in paeonol groups at 72 h (P < 0.05). In addition, histopathological analyses showed that the lesion in liver, spleen and caudal kidney were considerably attenuated in paeonol groups. In conclusion, paeonol could increase the survival rate, mitigate oxidative damage, inflammation, tissue lesions, and improve the immunity of gibel carp challenged with A. hydrophila.

关键词： Carassius auratus gibelio Paeonol Immune response Antioxidant capacity Inflammation

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Aquaponics model can provide better productivity: Microorganisms affect the growth and health of tilapia

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AQUACULTURE REPORTS 2025年 40卷

作者： Fan, Dingyue Xu, Huimin Meng, Shunlong Fan, Limin Song, Chao Qiu, Liping Li, Dandan Fang, Longxiang Liu, Zhuping bing, xuwen Shanghai Ocean Univ Coll Fisheries & Life Sci Shanghai Peoples R China Chinese Acad Fishery Sci Freshwater Fisheries Res Ctr Sci Observing & Expt Stn Fishery Resources & Envir Wuxi 214081 Peoples R China

Aquaponics is a novel ecological agricultural strategy that combines aquaculture and hydroponic cultivation. The relationships between fish immunological and digestive functions, water quality, and bacterial populations were not well understood. This study aims to investigate the effects of aquaponics on aquaculture water quality, fish growth performance, and fish health, as well as exploring the roles of microbial taxa in these processes. In the present study, three aquaponics systems were established, and three same sized recirculating aquaculture systems (RAS) were constructed to act as controls. To evaluate bacterial community diversity and compositions across different microhabitats in the two systems, we used amplicon-based high-throughput sequencing technique targeting the 16S rRNA gene. In aquaponics, fish had a much greater nitrogen utilization rate, weight gain rate (WGR), feed conversion ratio (FCR), and specific growth rate (SGR) than in controls. The activities of alkaline phosphatase (AKP), acid phosphatase (ACP), lysozyme (LYS), lipase (LPS), and trypsin (TRP) in tissues, all of which are indicators of fish health, were significantly greater in aquaponics than in controls. Aquaponics effectively lowered chlorophyll-a levels while having little effect on other water quality metrics, indicating their potential for better algae control. Water quality measures such as dissolved organic carbon, chlorophyll-a, dissolved oxygen, and ammonia nitrogen had a substantial impact on the fish's immunological and digestive capabilities. In terms of microbial influence, particular gut bacteria-such as the bacterial orders Pseudomonadales, Caulobacterales, Defluviicoccales, Exiguobacterales, and Gemmatales-have been identified as influencing various functions in fish. Among these bacterial orders, we found that Pseudomonadales and Exiguobacterales were more abundant in aquaponics than control systems. This study demonstrated that aquaponics can increase fish health an

关键词： Aquaponics Tilapia growth and health Water quality Microbial community

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Characterization of the growth-related transcriptome in the Liver and Brain of mandarin fish (Siniperca chuatsi) through RNA-Seq analysis

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JOURNAL OF APPLIED ANIMAL RESEARCH 2024年第1期52卷

The brain and liver of mandarin fish (Siniperca chuatsi) produce essential hormones for their growth and development. However, the mechanisms underlying the interplay of these hormones remain unclear. This study aimed to assess the slow - and fast-growing traits, including body weight and length of mandarin fish reared in a single pond. To compare the differentially expressed genes (DEGs) in slow - and fast-growing fishes, we performed RNA sequencing analysis. After assembling the clean reads, 192,280 transcripts and 100,416 unigenes were obtained. 344 and 845 DEGs in the brain and liver in the fast-and slow-growing group were annotated respectively. These DEGs were associated with signaling pathways involved in growth and development, such as AGE-RAGE, Transforming growth factor-beta/Smad, Mitogen-activated protein kinase, Wingless/Integrated, and Insulin-like growth factor (IGF) 1. Furthermore, our fasting experiment revealed a concurrent decrease in body weight and the expression levels of genes related to the growth hormone (GH)/IGF system, alongside an increase in the insulin-like growth factor binding protein gene IGFBP3 expression. These findings suggest the GH/IGF system regulates body weight during fasting periods. The vast amount of transcriptome data generated in this study substantially expands the existing gene and genome resources for the growth traits of mandarin fish.

关键词： Mandarin fish transcriptome growth DEG fasting

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Influences of Community Coalescence on the Assembly of Bacterial Communities of the Small-Scale Complex Aquatic System from the Perspective of Bacterial Transmission, Core Taxa, and Co-occurrence Patterns

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MICROBIAL ECOLOGY 2024年第1期87卷 145页

作者： Xu, Huimin Zhang, Yi Fan, Dingyue Meng, Shunlong Fan, Limin Song, Chao Qiu, Liping Li, Dandan Fang, Longxiang Liu, Zhuping bing, xuwen Chinese Acad Fishery Sci Freshwater Fisheries Res Ctr Wuxi 214081 Peoples R China Minist Agr & Rural Affairs Lab Qual & Safety Risk Assessment Aquat Prod Envir Wuxi 214081 Peoples R China Taihu Basin Author Minist Water Resource Water Conservancy Dev Res Ctr Shanghai 200438 Peoples R China Shanghai Ocean Univ Coll Fisheries & Life Sci Shanghai 201306 Peoples R China

Recirculating aquaculture and aquaponics are considered sustainable aquaculture models playing important roles in animal-derived protein supply. In these aquaculture systems, microorganisms are crucial for the system stability. The community coalescence by mixing substances and microorganisms from various microhabitats under hydraulic forces is important for shaping the bacterial communities in these small-scale complex systems. However, the influences of community coalescence on bacterial communities remain rarely revealed in these systems. In this study, aquaponics (APS) and recirculating aquaculture (RAS) systems were set up to explore the bacterial community coalescence across different microhabitats, including water, fish feces, biofilter biofilms, and plant rhizosphere environment. Our results showed that diversity and compositions varied across different microhabitats in both systems. However, bacterial transmissions across these microhabitats differed between systems. The core microbiome of the RAS and APS were formed under community coalescence with the highest contribution of bacterial taxa derived from the fish feces. Nevertheless, the plant rhizosphere bacterial community also contributed to the core microbiome of the APS. Furthermore, the core taxa showed a higher average degree than the other nodes in the bacterial community networks in all microhabitats except for the plant rhizosphere environment, implying the important roles of core taxa in maintaining these bacterial community networks. Our results provide new insights into the assembly of bacterial communities under community coalescence in the artificial aquatic ecosystems comprising complex microhabitats, which is vital for developing microbial solutions for regulating the microbial communities to improve system performance in the future.

关键词： Aquaponics Microhabitats Community coalescence Bacterial transmission Core taxa Co-occurrence network

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Experimental Study on the Inhibition of Bacteria and Algae by Jussiaea stipulacea Ohwi Extract

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NATURAL PRODUCT COMMUNICATIONS 2022年第9期17卷

作者： Shi, Yulu Zheng, Yao bing, xuwen Yuan, Julin Nanjing Agr Univ Wuxi Fishery Coll Wuxi Jiangsu Peoples R China Chinese Acad Fishery Sci CAFS Freshwater Fisheries Res Ctr Key Lab Integrated Rice Fish Farming Ecol Minist Agr & Rural Affairs Wuxi Jiangsu Peoples R China Minist Agr & Rural Affairs Key Lab Hlth Freshwater Aquaculture 999 Hangchangqiao Rd Huzhou 313001 Zhejiang Peoples R China Zhejiang Inst Freshwater Fisheries Key Lab Fish Hlth & Nutr Zhejiang Prov 999 Hangchangqiao Rd Huzhou 313001 Zhejiang Peoples R China

Nowadays, plant allelopathy, as a new type of biological algal and/or bacterial inhibition technology, has attracted extensive attention. Eight substances were isolated and identified from Jussiaea stipulacea Ohwi, and five concentration gradients, as well as a control (0, 1.25, 5, 10, 20, and 50 mg/L) were set, with three parallels in each group, and then sampled and detected at 24, 48, 72, and 96 h. When the concentration was 50 mg/L, the inhibition rate of Anabaena was as high as 74.8%, 69.2%, and 70.7% for ursolic acid, kaempferol, and luteolin, respectively. Streptococcus iniae and Aeromonas hydrophila were cultured to a logarithmic phase, and their final concentrations reached 1000, 500, 250, 125, 62.50, 31.25, 15.63, and 7.81 mu g/mL. Luteolin and gallic acid showed an inhibitory effect on S iniae and A hydrophila at 1000 mu g/mL. We found that allelochemicals also had a certain bacteriostatic effect, among which luteolin has great development potential.

关键词： allelopathic substances Jussiaea stipulacea Ohwi erythromycin florfenicol bacteriostatic and algal control

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Development and validation of a PCR-RFLP / TaqMan MGB probe method for rapid sex identification of largemouth bass (Micropterus salmoides)

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AQUACULTURE REPORTS 2023年 30卷

作者： Hua, Jixiang Qiang, Jun Tao, Yifan Li, Yan Lu, Siqi bing, xuwen Nanjing Agr Univ Wuxi Fisheries Coll Wuxi 214081 Peoples R China Chinese Acad Fishery Sci Freshwater Fisheries Res Ctr Key Lab Freshwater Fisheries & Germplasm Resources Minist Agr & Rural Affairs Wuxi 214081 Peoples R China

The largemouth bass (Micropterus salmoides) has become an important freshwater fish in China since it was intentionally introduced in the 1980 s, and the amount produced in aquaculture is increasing each year. Females are preferred because they grow faster than males and reach a larger body size. However, the physiological sex cannot be accurately determined from external morphology at the early growth stage, so it is crucial to develop sex-specific molecular markers. In this study, a single nucleotide polymorphism (SNP) marker was developed based on whole genome resequencing data obtained from 30 females and 30 males. This marker made it possible to positively identify male and female largemouth bass. Through Fst value screening, 123 SNP loci significantly associated with sex were obtained, and nearly 40% of them were located on chromosome 7 in a 3.44-Mb sex-linked region. A method of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) combined with a TaqMan minor groove binder (MGB) probe was developed based on a sex-specific marker. Using this method, male and female fish in four different populations (n = 128) were identified with 100% accuracy. Compared with PCR-RFLP followed by electrophoretic separation of fragments, the PCR-RFLP-TaqMan MGB probe method reduced the time required to identify the sex of largemouth bass. The validation results also indicated that largemouth bass has an XX/XY sex-determination system. In conclusion, we have identified a sex-specific SNP marker for largemouth bass and developed a new technique to identify the sex of largemouth bass rapidly and accurately. These findings provide a scientific basis for further research on mono-sex breeding and the molecular mechanism of sex determination in largemouth bass.

关键词： Largemouth bass Whole genome resequencing Sex-specific SNP Genetic sex identification

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Transcriptome analysis of blood for the discovery of sex-related genes in ricefield eelMonopterus albus

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FISH PHYSIOLOGY AND BIOCHEMISTRY 2020年第4期46卷 1507-1518页

作者： Ding, Weidong Cao, Liping Cao, Zheming bing, xuwen Chinese Acad Fishery Sci Key Lab Freshwater Fisheries & Germplasm Resource Minist Agr Freshwater Fisheries Res Ctr Wuxi 214081 Jiangsu Peoples R China

The blood acts as a transfer channel for a variety of factors in the whole body. The ricefield eel(Monopterus albus) is a protogynous hermaphrodite vertebrate. Until now, no research has reported an analysis of the blood transcriptome during the process of sexual development in the ricefield eel. In this study, the transcriptome sequencing of blood samples from male and female ricefield eels was completed with a total of 34.70 Gb clean data. The clean data of each sample all reached 5.23 GB, and the percent of the Q30 basic group was 88.62% and above. A total of 106,369 unigenes were obtained after assembly, including 13,296 unigenes with a length of more than 1 kb. Further functional annotation analysis showed that there are 28,522 unigenes that can be annotated. The annotations of genes with differential expression revealed that there were 563 genes with significant differential expression in the blood of male and female ricefield eels, including 91 upregulated genes and 472 downregulated genes. Among which, 14 genes may be closely related to sex differentiation, the qPCR was used to confirmed the expression pattern of those genes and result shown that 11 genes were downregulated and 3 genes were upregulated, consistent with the results of our RNA-Seq analysis. This blood transcript dataset will open future research avenues on ricefield eel sex development and differentiation.

关键词： Blood Transcriptome Sex development genes Ricefield eel

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Protective effects of paeonol against lipopolysaccharide-induced liver oxidative stress and inflammation in gibel carp (Carassius auratus gibelio)

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COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY 2022年第0期257卷 109339页

作者： Gu, Yipeng Chen, Kai Xi, bingwen Xie, Jun bing, xuwen Nanjing Agr Univ Wuxi Fisheries Coll Shanshui East Rd 9 Wuxi 214081 Jiangsu Peoples R China Chinese Acad Fishery Sci Freshwater Fisheries Res Ctr Key Lab Freshwater Fisheries & Germplasm Resource Minist Agr & Rural Affairs Wuxi 214081 Jiangsu Peoples R China

Paeonol (2'-hydroxy-4'-methoxyacetophenone) is a phenol that exhibits antioxidant and anti-inflammatory capabilities. In this study, the underlying mechanism of paeonol against LPS-induced oxidative stress and inflammatory responses in gibel carp was investigated. Three hundred healthy gibel carp were divided into five groups (n = 9), intraperitoneally injected with LPS and thereafter treated with paeonol (16 mg/kg and 64 mg/kg). Fish were anesthetized with MS-222 (100 mg/L), and samples were collected at 72 h to investigate plasma biochemical indexes, liver histopathology, antioxidant enzymatic activity, and TLR receptor-related gene expression. Fish injected with LPS (20 mg/kg) exhibited significantly increased plasma aminotransferase (ALT), aminotransferase (AST), lactate dehydrogenase (LDH), glucose (GLU), diamine oxidase (DAO), and alkaline phosphatase (ALP) levels (P < 0.05). In addition, LPS challenge significantly enhanced myeloperoxidase (MPO) and malondialdehyde (MDA) contents, whereas those of catalase (CAT) and glutathione peroxidase (GSH-Px) decreased (P < 0.05). However, treatment with paeonol attenuated these LPS-induced changes (P < 0.05). The mRNA expression of TLR4, TIRAP, MyD88, TRAF6, NF-kappa B, TNF-alpha, IL-1 beta, and IL-8, which were activated by LPS challenge (P < 0.05), were downregulated by paeonol. Additionally, histopathological examination demonstrated that paeonol alleviates LPS-induced hepatic tissue lesions in fish. Taken together, the results suggest that paeonol mitigates LPS-induced liver oxidative stress and inflammation in gibel carp.

关键词： Paeonol Carassius auratus gibelio Lipopolysaccharide Oxidative stress Inflammation

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