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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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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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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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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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Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var. Jian

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GENETICA 2016年第3期144卷 325-333页

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

A Ty3/gypsy-retrotransposon-type transposon was found in the genome of the Jian carp (Cyprinus carpio var. Jian) in a previous study (unpublished), and was designated a JRE retrotransposon (Jian retrotransposon). The full-length JRE retrotransposon is 5126 bp, which includes two long terminal repeats of 470 bp at the 5' end and 453 bp at the 3' end, and two open reading frames between them: 4203 bp encoding the group-specific antigen (GAG) and polyprotein (POL). The pol gene has a typical Ty3/gypsy retrotransposon structure, and the gene order is protease, reverse transcriptase, RNase H, and integrase (PR-RT-RH-IN). A phylogenetic analysis of the pol gene showed that it has similarities of 40.7, 40, and 32.8 %, to retrotransposons of Azumapecten farreri, Mizuhopecten yessoensis, and Xiphophorus maculatus, respectively. Therefore, JRE might belong to the JULE retrotransposon family. The copy number of the JRE transposon in the genome of the Jian carp is 124, determined with real-time quantitative PCR. The mRNA of the JRE retrotransposon is expressed in five Jian carp tissues, the liver, kidney, blood, muscle, and gonad, and slightly higher in the kidney and liver than in the other tissues.

关键词： Cyprinus carpio var. Jian Retrotransposon Copy number Fluorescent in situ hybridization

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Non-O1 Vibrio cholerae pathogen from Cyprinus carpio and control with anti-non-O1 V. cholerae egg yolk powder (IgY)

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AQUACULTURE 2017年 479卷 69-74页

作者： Gao, Xiaojian Chen, Nan Zhang, Yue Zhang, Xiaojun bing, xuwen Yangzhou Univ Coll Anim Sci & Technol Yangzhou Jiangsu Peoples R China Chinese Acad Fishery Sci Minist Agr Freshwater Fisheries Res Ctr Key Lab Freshwater Fisheries & Germplasm Utilizat Wuxi Peoples R China

Mass mortality in cultured common carp from a farm of Ganyu county, Jiangsu province, P. R. China was reported. The two dominated isolates named L1 and L2 from diseased common carps were confirmed as non-O1 Vibrio cholerae by biochemical characteristics and molecular tools. Virulence genes (ompW, hlyA, acfA, toxR, ace and rtxC genes) were found to be present in the isolates by PCR, which further confirmed pathogenicity of the isolates. The LD50 value of the isolate L1 to the common carp was 1.1 x 10(6) CFU/mL. In addition, the specific egg yolk powder (IgY) conferred significant protection of common carp against non-O1 V. cholerae. The specific IgY also exhibited significant bacteriolytic effects on the non-O1 V. cholerae pathogen. The results showed that the specific IgY should be an effective implemented feed additive for the biocontrol of non-O1 V. cholerae infection in aquaculture.

关键词： Cyprinus carpio Non-O1 Vibrio cholerae Virulence gene Egg yolk powder (IgY)

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Time-dependent gut microbiota analysis of juvenile Oreochromis niloticus by dietary supplementation of resveratrol

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ARCHIVES OF MICROBIOLOGY 2020年第1期202卷 43-53页

作者： Zheng, Yao Hu, Gengdong Wu, Wei Qiu, Liping bing, xuwen Chen, Jiazhang Chinese Acad Fishery Sci Fishery Ecoenvironm Monitoring Ctr Lower Reaches Freshwater Fisheries Res Ctr Minist AgrLab Qual & Safety Risk Assessment Aqua 9 Shanshui East Rd Wuxi 214081 Jiangsu Peoples R China Minist Agr Key Lab Control Qual & Safety Aquat Prod Beijing 100141 Peoples R China

To evaluate the changes in bacterial diversity at various time points under resveratrol supplementation, we aimed to investigate the diversification of gut microbiota and the changes in total genetic diversity. We performed 16S rDNA gene sequencing at different time points (15, 30, and 45 days) to analyze the gut microbiota of tilapia. Fusobacteria, Proteobacteria, and Bacteroidetes (15 days) or Cyanobacteria (30 and 45 days) were found to be the three most abundant phyla. Cyanobacteria (15 and 30 days), Proteobacteria (15 days), Firmicutes and Chlamydiae (30 and 45 days), Planctomycetes (30 days), Bacteroidetes, Actinobacteria, and Fusobacteria (45 days) in the 0.05 g/kg RES group increased as compared to that in the controls. Proteobacteria and Cyanobacteria significantly decreased and increased at 30 and 45 days, respectively, while the reverse pattern was observed at 15 days. The Bacteroidetes:Firmicutes and Proteobacteria:Cyanobacteria ratios were significantly increased (15 and 45 days, P < 0.05) and decreased (30 days, P < 0.05). RES supplementation did not affect the richness and diversity of the gut microbiota in tilapia. Our findings may contribute to the development of strategies for the management of diseases.

关键词： Resveratrol GIFT Gut microbiota 16S rDNA Chinese medical herbs

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Varieties of immunity activities and gut contents in tilapia with seasonal changes

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FISH & SHELLFISH IMMUNOLOGY 2019年 90卷 466-476页

作者： Zheng, Yao Wu, Wei Hu, Gengdong Qiu, Liping bing, xuwen Chen, Jiazhang Chinese Acad Fishery Sci Freshwater Fisheries Res Ctr 9 Shanshui East Rd Wuxi 214081 Jiangsu Peoples R China

We performed 16S rDNA sequencing of tilapia fecal samples to analyze changes in tilapia gut contents after cultivation of the fish in the presence of sandwich-like floating beds of Chinese medicinal herbs (5 and 10% planting-areas;5% Polygonum cuspidatum). The interactive effects between water quality and blood and hepatic pro- and anti-inflammatory concentrations were also assessed. Our results showed that the water quality (i.e., NO3--N, NO2--N, TP removal rates) improved, and the abundance of Chloroflexi and Cyanobacteria increased. The abundance of Bacteroidetes, Verrucomicrobia, Saccharibacteria, and Actinobacteria showed both significant seasonal decreases and increases in the presence of P. cuspidatum (increases in August and decreases in July). Fish blood and hepatic IL-10 and IFN-gamma levels (together with fish sampled in September) significantly increased in the P. cuspidatum group sampled in August, while those of TNF-alpha (10% sandwich-like, P. cuspidatum), IL-1 beta (P. cuspidatum), IL-8 (5% sandwich-like in September, S905S) significantly decreased. Heat shock proteins 60 and 70 levels significantly increased in the P. cuspidatum group, and complement C3 and C4 concentrations significantly increased in S905S. This study demonstrated that enhanced immunity through the regulation of pro- and anti-inflammatory proteins was sustained throughout development until harvest, particularly in fish grown with P. cuspidation.

关键词： Tilapia Gut contents Floating bed cultivation 16S rDNA Disease

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Reshaping fecal gut microbiota composition by growing with Polygonum cuspidatum, Houttuynia cordata, and Ipomoea aquatica

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CANADIAN JOURNAL OF MICROBIOLOGY 2019年第7期65卷 522-529页

作者： Zheng, Yao Hu, Gengdong Wu, Wei Qiu, Liping Li, Dandan bing, xuwen Chen, Jiazhang Chinese Acad Fishery Sci Freshwater Fisheries Res Ctr Wuxi Jiangsu Peoples R China

We carried out sequencing of samples cultivated in floating beds with different Chinese medicinal herbs (Control, Houttuynia cordata Thunb., Polygonum cuspidatum, and a combination of H. cordata with Ipomoea aquatica Forssk.;named groups A, B, C, D, respectively) to analyze changes in the composition of gut microbiota of tilapia feces. Fusobacteria (ranging from 49.0% to 73.3%), Firmicutes (12.3%-37.8%), and Proteobacteria (5.1%-23.0%) were found to be the most dominant phyla present in all samples. The operational taxonomic units and the Ace and Chao1 indices of groups A and D were significantly higher than those of group C. Polygonum cuspidatum decreased the species richness and diversity of microbial communities in tilapia intestinal feces. The phylum WCHB1-60, order Enterobacteriales, and genus Plesiomonas significantly decreased (in group A);the species Plesiomonas shigelloides significantly decreased (in groups B and C);and the genus Leucobacter significantly increased (in group D) when compared with the control. The relative abundance of the class Verrucomicrobiae (groups B vs C) significantly decreased. In the presence of I. aquatica, the phylum Bacteroidetes significantly decreased, while the genera Leucobacter and Pelotomaculum significantly increased. The ratio of Bacteroidetes to Firmicutes was significantly higher in groups B and C relative to the controls, while it decreased significantly in group D. The algae (i. e., Anabaena and Microcystis) and beneficial pathogenic bacteria decreased in groups C and D, respectively. In addition, Enterovibrio decreased in all treatment groups. The present data demonstrate that floating bed cultivation with Chinese medicinal herbs significantly alters the gut microbiota of tilapia, which may enhance its immune activity.

关键词： tilapia fecal gut microbiota floating bed cultivation 16S rDNA disease

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