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Li P, Liu W, Lu W, Wang J. Biochemical indices, gene expression, and SNPs associated with salinity adaptation in juvenile chum salmon ( Oncorhynchus keta) as determined by comparative transcriptome analysis. PeerJ 2022; 10:e13585. [PMID: 36117540 PMCID: PMC9477081 DOI: 10.7717/peerj.13585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/23/2022] [Indexed: 01/17/2023] Open
Abstract
Chum salmon (Oncorhynchus keta) migrate from freshwater to saltwater, and incur developmental, physiological and molecular adaptations as the salinity changes. The molecular regulation for salinity adaptation in chum salmon is currently not well defined. In this study, 1-g salmon were cultured under 0 (control group, D0), 8‰ (D8), 16‰ (D16), and 24‰ (D24) salinity conditions for 42 days. Na+/K+-ATPase and Ca2+/Mg2+-ATPase activities in the gill first increased and then decreased in response to higher salinity environments where D8 exhibited the highest Na+/K+ATPase and Ca2+/Mg2+-ATPase activity and D24 exhibited the lowest. Alkaline phosphatase (AKP) activity was elevated in all salinity treatment groups relative to controls, while no significant difference in acid phosphatase (ACP) activity was observed across treatment groups. De novo transcriptome sequencing in the D0 and D24 groups using RNA-Seq analysis identified 187,836 unigenes, of which 2,143 were differentially expressed in response to environmental salinity (71 up-regulated and 2,072 down-regulated). A total of 56,020 putative single nucleotide polymorphisms (SNPs) were also identified. The growth, development, osmoregulation and maturation factors of N-methyl-D-aspartate receptors (nmdas) expressed in memory formation, as well as insulin-like growth factor 1 (igf-1) and igf-binding proteins (igfbps) were further investigated using targeted qRT-PCR. The lowest expression of all these genes occurred in the low salinity environments (D8 or D16), while their highest expression occurred in the high salinity environments (D24). These results provide preliminary insight into salinity adaptation in chum salmon and a foundation for the development of marker-assisted breeding for this species.
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Affiliation(s)
- Peilun Li
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Harbin, China
| | - Wei Liu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Harbin, China
| | - Wanqiao Lu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Harbin, China
| | - Jilong Wang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China,Key Open Laboratory of Cold Water Fish Germplasm Resources and Breeding of Heilongjiang Province, Heilongjiang River Fisheries Research Institute, Harbin, China
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Genome-wide integrated analysis reveals functions of lncRNA-miRNA-mRNA interactions in Atlantic salmon challenged by Aeromonas salmonicida. Genomics 2021; 114:328-339. [PMID: 34933071 DOI: 10.1016/j.ygeno.2021.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/01/2021] [Accepted: 12/15/2021] [Indexed: 12/25/2022]
Abstract
Aeromonas salmonicida (A. salmonicida) is a pathogenic bacterium that causes serious problems in the global Atlantic salmon aquaculture industry. In this study, we comprehensively analyzed the profiles of lncRNAs, miRNAs and mRNAs in gills of Atlantic salmon at high-dose A. salmonicida infection (3.06 × 108 CFU/mL), low-dose A. salmonicida infection (3.06 × 105 CFU/mL), and a PBS (100 μL) control. We identified 65 differentially expressed lncRNAs, 41 miRNAs, and 512 mRNAs between the control group and infection groups. Functional analysis showed that these genes were significantly enriched in the p53 signaling pathway, Wnt signaling pathway, mTOR signaling pathway, JAK-STAT signaling pathway, and Toll-like receptor signaling pathway. In addition, we predicted key genes in immune-related pathways and constructed a lncRNA-miRNA-mRNA network based on whole transcriptomic analysis. We further predicted three lncRNA-miRNA-mRNA axes as potential novel biomarkers in regulating the immune response of Atlantic salmon against A. salmonicida infection.
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Zhou QL, Xia D, Pan L, Wang J, Chen Q, Ge X, Sun C, Miao L, Lin Y, Liu B. Molecular cloning and expression mechanism of Mnp65 in Megalobrama amblycephala response to Aeromonas hydrophilia challenge. Comp Biochem Physiol A Mol Integr Physiol 2021; 261:111046. [PMID: 34352395 DOI: 10.1016/j.cbpa.2021.111046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 01/11/2023]
Abstract
p65 is one of the important subunits of the inflammation-related transcription factor NF-κB. In the present study, we cloned and identified the p65 from Megalobrama amblycephala (Mnp65) by homologous cloning and RACE technique. The full-length Mnp65 cDNA consisted of 2331 bp, and included one open reading frame encoding a 604-amino acid putative protein. The protein sequence included a DNA binding motif, a well conserved N-terminal Rel-homology domain (RHD), and a C-terminal IG-like plexins transcription (IPT). Mnp65 was closely related with the other p65 proteins of Cypriniformes and clearly distinct from that of Perciformes and Salmoniformes in terms of sequence homology. Mnp65 homodimer may interact with IκBα in the IPT domain based on the predicted 3D structure of IκBα/Mnp65 complex. Mnp65 was ubiquitously expressed in M. amblycephala tissues, and the highest levels were detected in muscle and liver. Intragastric infection with Aeromonas hydrophila caused respiratory burst and cytokine storm from 8 h to 48 h, showing significantly higher level of respiratory burst activities and significantly high cytokines levels, such as TNF-α, IL-1β, IL-6, IL-8 etc., compared to 0 h. In addition, the bacterial challenge downregulated the IkBα, and upregulated Mnp65 and TNF-α in the liver. IkBα-Mnp65 was regulated by the negative feedback of cytokine storm, to increase IkBα and decrease Mnp65. Then cytokine storm was relieved at 96 h. Finally, severe intestinal inflammation was observed from 24 h to 48 h after infection, characterized by extensive villous necrosis, epithelial hyperplasia and lymphocyte infiltration, all of which were relieved at 96 h. Taken together, Mnp65 plays a crucial role in the physiological response of teleost fish to bacterial infection.
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Affiliation(s)
- Qun-Lan Zhou
- Key Laboratory for Genetic Breeding of Aquatic Animals and Aquaculture Biology, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Shanshui East Road No. 9, Wuxi, Jiangsu 214081, PR China; Wuxi Fisheries College, Nanjing Agricultural University, Shanshui East Road No. 9, Wuxi, Jiangsu 214081, PR China
| | - Dong Xia
- Key Laboratory for Genetic Breeding of Aquatic Animals and Aquaculture Biology, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Shanshui East Road No. 9, Wuxi, Jiangsu 214081, PR China
| | - Liangkun Pan
- Key Laboratory for Genetic Breeding of Aquatic Animals and Aquaculture Biology, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Shanshui East Road No. 9, Wuxi, Jiangsu 214081, PR China
| | - Jingyuan Wang
- Nanjing Alpha Feed Biological Technology Co., Ltd., Binhuai Avenue No.9, Nanjing, Jiangsu 211200, PR China
| | - Qian Chen
- Wuxi Fisheries College, Nanjing Agricultural University, Shanshui East Road No. 9, Wuxi, Jiangsu 214081, PR China
| | - Xianping Ge
- Key Laboratory for Genetic Breeding of Aquatic Animals and Aquaculture Biology, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Shanshui East Road No. 9, Wuxi, Jiangsu 214081, PR China; Wuxi Fisheries College, Nanjing Agricultural University, Shanshui East Road No. 9, Wuxi, Jiangsu 214081, PR China
| | - Cunxin Sun
- Key Laboratory for Genetic Breeding of Aquatic Animals and Aquaculture Biology, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Shanshui East Road No. 9, Wuxi, Jiangsu 214081, PR China
| | - Linghong Miao
- Key Laboratory for Genetic Breeding of Aquatic Animals and Aquaculture Biology, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Shanshui East Road No. 9, Wuxi, Jiangsu 214081, PR China; Wuxi Fisheries College, Nanjing Agricultural University, Shanshui East Road No. 9, Wuxi, Jiangsu 214081, PR China
| | - Yan Lin
- Key Laboratory for Genetic Breeding of Aquatic Animals and Aquaculture Biology, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Shanshui East Road No. 9, Wuxi, Jiangsu 214081, PR China
| | - Bo Liu
- Key Laboratory for Genetic Breeding of Aquatic Animals and Aquaculture Biology, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Shanshui East Road No. 9, Wuxi, Jiangsu 214081, PR China; Wuxi Fisheries College, Nanjing Agricultural University, Shanshui East Road No. 9, Wuxi, Jiangsu 214081, PR China.
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Chen J, Liu N, Li B, Zhang H, Zhao Y, Cao X. The effects of fipronil exposure on oxidative stress, non-specific immunity, autophagy, and apoptosis in the common carp. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:27799-27810. [PMID: 33515409 DOI: 10.1007/s11356-021-12573-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
The increase in the area treated with the insecticide fipronil has caused concern for aquatic organisms such as fish. Here, we assessed the effect of fipronil on carp indexes of non-specific immunity, oxidative stress, autophagy, and apoptosis following exposure to 0.074 mg/L and 0.185 mg/L of fipronil in the aqueous environment for 1 day, 3 days, 5 days, and 7 days. It was found that glutathione (GSH), malonaldehyde (MDA), and superoxide dismutase (SOD) in gills were significantly reduced (P < 0.05). The increase in exposure time increases the impact on GSH, SOD, and MDA parameters in the liver and intestine. Liver acid phosphatase (ACP), alkaline phosphatase (AKP), and lysozyme (LZM) activity levels increased significantly in the treatment group on the first day after exposure, except for the 0.074 mg/L group of ACP (P < 0.05). The mRNA expression levels of autophagy-related genes ATG12, ATG5, ATG16L, LC3-II, and BECN1 were generally elevated in the liver and intestine during the initial exposure period (P < 0.05), while mTOR was significantly reduced on the first and third days after treatment (P < 0.05). From the results of Western blotting (WB), we can see that the amount of LC3-II was significantly higher than that of LC3-I at 1, 3, and 5 days of exposure (P < 0.05). Furthermore, the apoptosis-related gene Bcl-2 reached its peak in the liver, intestine, and gill on the first day, and caspase3 was significantly downregulated throughout the exposure period (P < 0.05). The results showed that fipronil was potentially harmful to carp and should be used moderately to reduce the damage to aquatic ecosystems. This study complements the mechanism theory of fipronil on fish toxicology and has a certain value for human health risk assessment.
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Affiliation(s)
- Jianjun Chen
- College of Life Science, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Nana Liu
- College of Life Science, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Baohua Li
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Huajie Zhang
- College of Life Science, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Yidi Zhao
- College of Life Science, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Xianglin Cao
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China.
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Zou S, Gong L, Khan TA, Pan L, Yan L, Li D, Cao L, Li Y, Ding X, Yi G, Sun Y, Hu S, Xia L. Comparative analysis and gut bacterial community assemblages of grass carp and crucian carp in new lineages from the Dongting Lake area. Microbiologyopen 2020; 9:e996. [PMID: 32175674 PMCID: PMC7221430 DOI: 10.1002/mbo3.996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 12/17/2022] Open
Abstract
Gut microbiota are known to play an important role in health and nutrition of the host and have been attracting an increasing attention. Farming of new lineages of grass carp and crucian carp has been developed rapidly as these species were found to outperform indigenous ones in terms of growth rate and susceptibility to diseases. Despite this rapid development, no studies have addressed the characteristics of their gut microbiota as a potential factor responsible for the improved characteristics. To reveal whether microbiomes of the new lineages are different from indigenous ones, and therefore could be responsible for improved growth features, intestinal microbiota from the new lineages were subjected to high-throughput sequencing. While the phyla Firmicutes, Fusobacteria and Proteobacteria were representing the core bacterial communities that comprised more than 75% in all fish intestinal samples, significant differences were found in the microbial community composition of the new linages versus indigenous fish populations, suggesting the possibility that results in the advantages of enhanced disease resistance and rapid growth for the new fish lineages. Bacterial composition was similar between herbivorous and omnivorous fish. The relative abundance of Bacteroidetes and Actinobacteria was significantly higher in omnivores compared to that of herbivores, whereas Cetobacterium_sp. was abundant in herbivores. We also found that the gut microbiota of freshwater fish in the Dongting lake area was distinct from those of other areas. Network graphs showed the reduced overall connectivity of gut bacteria in indigenous fish, whereas the bacteria of the new fish lineage groups showed hubs with more node degree. A phylogenetic investigation of communities by reconstruction of unobserved states inferred function profile showed several metabolic processes were more active in the new lineages compared to indigenous fish. Our findings suggest that differences in gut bacterial community composition may be an important factor contributing to the rapid growth and high disease resistance of the new fish lineages.
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Affiliation(s)
- Sheng Zou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liang Gong
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Tahir Ali Khan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Lifei Pan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liang Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Dongjie Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Lina Cao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Yanping Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Xuezhi Ding
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Ganfeng Yi
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Yunjun Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Shengbiao Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular BiologyCollege of Life ScienceHunan Normal UniversityChangshaChina
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Liu Z, Iqbal M, Zeng Z, Lian Y, Zheng A, Zhao M, Li Z, Wang G, Li Z, Xie J. Comparative analysis of microbial community structure in the ponds with different aquaculture model and fish by high-throughput sequencing. Microb Pathog 2020; 142:104101. [PMID: 32109568 DOI: 10.1016/j.micpath.2020.104101] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/24/2020] [Accepted: 02/24/2020] [Indexed: 01/19/2023]
Abstract
The pond has a complex microbial ecosystem, including microorganisms in water and sediment, which plays an important role in the health of fish and water quality. The microbial community structure in the ponds can be easily affected by many factors. However, not much is known about the role of different aquaculture model and fish on the microbial community structure in ponds. The purpose of the study was to investigate the microbial diversity and composition of the ponds with different aquaculture model and fish by high-throughput sequencing. A total of 3835072 valid sequences were achieved from 60 samples. Additionally, 2064 and 1917 core OTUs were observed in water and sediment samples, respectively. Our results suggested that sediment samples have a higher abundance and diversity of microbial community than water samples. In all the samples, the four most dominant phyla were Proteobacteria, Cyanobacteria, Actinomycetes and Bacteroides. At the genus level, hgcI_clade and CL500-29_marine_group were the dominant bacteria shared by the water samples and sediment samples. In addition, more bacteria related to eutrophication were found in the group of BF, BC and HSB, which suggested that these ponds may have been eutrophicated. In conclusion, the present study revealed the differences in the structure and diversity of microbial communities in ponds with different aquaculture model and fish. Furthermore, changes in typical bacteria of the ponds contribute to detect water quality and prevent water eutrophication.
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Affiliation(s)
- Zhigang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; College of Life Science, Anqing Normal University, Anqing, 246011, PR China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Mudassar Iqbal
- University College of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, 63100, Pakistan; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Zhibo Zeng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Yuxi Lian
- College of Life Science, Anqing Normal University, Anqing, 246011, PR China
| | - Aifang Zheng
- College of Life Science, Anqing Normal University, Anqing, 246011, PR China
| | - Mengmeng Zhao
- College of Life Science, Anqing Normal University, Anqing, 246011, PR China
| | - Zixin Li
- College of Life Science, Anqing Normal University, Anqing, 246011, PR China
| | - Guangjun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Zhifei Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China.
| | - Jun Xie
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China.
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