Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella)

Effects of Different Stocking Densities on Snail Bellamya purificata Foot Muscle Nutritional Quality and Metabolic Function

Snail Bellamya purificata is not only useful for bioremediation, purifying aquaculture environments, but it is also a commercially valuable and nutritionally rich aquatic product. To analyze the effect of various stocking densities on the muscle nutritional quality and metabolic functions of B. purificata. The transcriptome and metabolome were analyzed and set up three different density groups-low (LD, 234.38 g/m2), medium (MD, 468.75 g/m2), and high (HD, 937.5 g/m2). The results of the study showed that the weight gain (WG) and specific growth rate (SGR) of B. purificata in the MD and HD groups were significantly lower compared to the LD group. High stocking density significantly reduced the oleic acid (C18:1n9c), linoleic acid (C18:2n6c), alpha-linolenic acid (C18:3n3), eicosadienoic acid (C20:2), erucic acid (C22:1n9), docosahexaenoic acid (DHA, C22:6n3), and lignoceric acid (C24:0) levels within snail foot muscle. Most of the identified differentially expressed genes (DEGs) were categorized as Signal transduction, according to the Kyoto Encyclopedia of Genes and Genomes (KEGG); these genes were categorized into Transport and catabolism, Endocrine system, and Immune system. A total of 11 upregulated DEGs and 19 downregulated DEGs were identified and confirmed to be associated with density stress. The identified metabolites were mainly enriched in the Metabolism category, with 620 differential metabolites identified in positive ion (POS) mode and 265 differential metabolites identified in the negative ion (NEG) mode among different stocking density groups. The differential metabolites affected by stocking density were primarily amino acids, nucleic acids, vitamins, and lipid metabolites. There were 8 upregulated differential metabolites and 14 downregulated differential metabolites identified and confirmed to be associated with density stress. These findings elucidated the response mechanisms of B. purificata to adverse stocking density conditions and provide data and a theoretical basis for selecting appropriate stocking densities for B. purificata.

Occurrence, distribution and health risk assessment of quinolone residues in cultured fish in southeast China

Quinolone antibiotics are widely utilized in aquaculture, but little is known about the health effects of their residues. This study used UPLC-MS/MS to analyze the distribution of 11 quinolone antibiotics in cultured fish sold in a coastal city in southeast China - Fujian Province and to assess their health risks. The study found 35.77% of 260 cultured fish samples detected quinolones, with three exceeding the MRL and one containing the banned drug ofloxacin. Of the 11 quinolones tested, three were found in cultured fish, with enrofloxacin at up to 246.0 μg kg-1, followed by ciprofloxacin and ofloxacin. The distribution of antibiotic detection rates showed no significant differences across regions or time periods; however, notable variations were observed among different fish species. The dietary exposure assessment revealed that consuming cultured fish does not pose a health risk to residents. Nevertheless, there are still instances that exceed regulatory limits. Therefore, routine monitoring and risk assessment are essential for enhancing regulatory measures and protecting public health.

Influences of Stocking Density on Antioxidant Status, Nutrients Composition, and Lipid Metabolism in the Muscles of Cyprinus carpio under Rice-Fish Co-Culture

Cyprinus carpio is a significant freshwater species with substantial nutritional and economic value. Rice-carp co-culture represents one of its principal cultivation methods. However, in the system, the optimal farming density for carp and the impact of high stocking density on their muscle nutritional composition have yet to be explored. Thus, the objective of the current study was to investigate the influences of stocking density on the muscle nutrient profiles and metabolism of C. carpio in rice-fish co-culture systems. Common carp were cultured at three stocking densities, low density (LD), medium density (MD), and high density (HD), over a period of 60 days. Following this, comprehensive analyses incorporating physiological, biochemical, and multi-omics sequencing were conducted on the muscle tissue of C. carpio. The results demonstrated that HD treatment led to a reduction in the antioxidant capacity of C. carpio, while resulting in elevated levels of various fatty acids in muscle tissue, including saturated fatty acids (SFAs), omega-3 polyunsaturated fatty acids (n-3 PUFAs), and omega-6 polyunsaturated fatty acids (n-6 PUFAs). The metabolome analysis showed that HD treatment caused a marked reduction in 43 metabolites and a significant elevation in 30 metabolites, primarily linked to lipid and amino acid metabolism. Additionally, transcriptomic analysis revealed that the abnormalities in lipid metabolism induced by high-stocking-density treatment may be associated with significant alterations in the PPAR signaling pathway and adipokine signaling pathway. Overall, our findings indicate that in rice-fish co-culture systems, high stocking density disrupted the balance of antioxidant status and lipid metabolism in the muscles of C. carpio.

Transcriptome Analysis Reveals the Effect of Stocking Density on Energy Metabolism in the Gills of Cherax quadricarinatus under Rice-Crayfish Co-Culture

Stocking density is a crucial factor affecting productivity in aquaculture, and high stocking density is a stressor for aquatic animals. In this study, we aimed to investigate the effects of stocking densities on oxidative stress and energy metabolism in the gills of Cherax quadricarinatus under rice-crayfish farming. The C. quadricarinatus were reared at low density (LD), medium density (MD), and high density (HD) for 90 days. The results showed that the superoxide dismutase (SOD), catalase (CAT), glutathione (GSH), and malondialdehyde (MDA) levels were higher in the HD group than those in the LD group. Transcriptomic analysis revealed 1944 upregulated and 1157 downregulated genes in the gills of the HD group compared to the LD group. Gene ontology (GO) enrichment analysis indicated that these differentially expressed genes (DEGs) were significantly associated with ATP metabolism. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis also showed that high stocking density resulted in the dysregulation of oxidative phosphorylation. Furthermore, high stocking density upregulated six lipid metabolism-related pathways. Overall, our findings, despite the limited number of samples, suggested that high stocking density led to oxidative stress and dysregulation of energy metabolism in the gills of C. quadricarinatus under rice-crayfish co-culture. Alteration in energy metabolism may be an adaptive response to adverse farming conditions.

Identification of multifunctionality of grass carp (Ctenopharyngodon idella) TBK1 during bacterial infection

TBK1 is an atypical IκB kinase family member with a set of functions. It is involved in congenital immunization and autophagy in mammals. In this study, we reported that grass carp TBK1 gene expression could be upregulated by bacterial infection. Overexpression of TBK1 could decrease the number of adhesive bacteria in CIK cells. TBK1 could promote cellular migration, proliferation, vitality, and anti-apoptosis ability. Furthermore, the expression of TBK1 could activate the NF-κB signaling pathway by inducing inflammatory cytokines. In addition, we found that the grass carp TBK1 could cause the autophagy level of CIK cells within the decreasing level of p62 protein. Our finding indicated that TBK1 participated in grass carp innate immune progress and autophagy. This study provides evidence of the positive regulation of TBK1 in teleost innate immunity with its multiple functions. It thus may provide important information about the defense and immune mechanisms used by teleost against pathogens.

Effects of stocking density on the growth performance, mitophagy, endocytosis and metabolism of Cherax quadricarinatus in integrated rice-crayfish farming systems

Red claw crayfish (Cherax quadricarinatus) is an economic freshwater shrimp with great commercial potential. However, the suitable stocking density of C. quadricarinatus is still unclear in integrated rice-crayfish farming system. Thus, this study aimed to investigate the effects of stocking density on growth performance, mitophagy, endocytosis and metabolism of C. quadricarinatus. The C. quadricarinatus was reared at low density (LD, 35.73 g/m²), middle density (MD, 71.46 g/m²) and high density (HD, 107.19 g/m²) in an integrated rice-crayfish farming system. After 90 days of farming, the growth performance of C. quadricarinatus significantly decreased in the MD and HD groups relative to that in the LD group. The HD treatment caused oxidative stress and lipid peroxidation at the end of the experiment in hepatopancreas. Transcriptome analysis showed that there were 1,531 DEGs (differently expressed genes) between the LD group and HD group, including 1,028 upregulated genes and 503 downregulated genes. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis indicated that the DEGs were significantly enriched in endocytosis and mitophagy pathways. Meanwhile, four lipid metabolism pathways, including biosynthesis of unsaturated fatty acids, fatty acid biosynthesis, glycerolipid metabolism and glycerophospholipid metabolism, exhibited an upregulated tendency in the HD group. In conclusion, our data showed that when the stocking density reached up to 207.15 g/m² in HD group, the growth performance of C. quadricarinatus was significantly inhibited in this system. Meanwhile, the data indicated that C. quadricarinatus may respond to the stressful condition via activating antioxidant defense system, endocytosis, mitophagy and metabolism-related pathways in hepatopancreas.

Dynamic Transcriptional Landscape of Grass Carp (Ctenopharyngodon idella) Reveals Key Transcriptional Features Involved in Fish Development

A high-quality baseline transcriptome is a valuable resource for developmental research as well as a useful reference for other studies. We gathered 41 samples representing 11 tissues/organs from 22 important developmental time points within 197 days of fertilization of grass carp eggs in order to systematically examine the role of lncRNAs and alternative splicing in fish development. We created a high-quality grass carp baseline transcriptome with a completeness of up to 93.98 percent by combining strand-specific RNA sequencing and single-molecule real-time RNA sequencing technologies, and we obtained temporal expression profiles of 33,055 genes and 77,582 transcripts during development and tissue differentiation. A family of short interspersed elements was preferentially expressed at the early stage of zygotic activation in grass carp, and its possible regulatory components were discovered through analysis. Additionally, after thoroughly analyzing alternative splicing events, we discovered that retained intron (RI) alternative splicing events change significantly in both zygotic activation and tissue differentiation. During zygotic activation, we also revealed the precise regulatory characteristics of the underlying functional RI events.

Effects of Stocking Density on the Growth Performance, Physiological Parameters, Redox Status and Lipid Metabolism of Micropterus salmoides in Integrated Rice–Fish Farming Systems

Stocking density has been identified as one of the main factors affecting fish growth, welfare and behavior. However, few studies have focused on the effects of stocking density on fish health in integrated rice–fish farming systems. Thus, the aim of this study was to evaluate the effects of different stocking densities on the growth performance, physiological parameters, redox status and lipid metabolism of Micropterus salmoides in an integrated rice–fish farming system. The fish were reared at three densities: low density (LD, 40 g/m³), medium density (MD, 80 g/m³) and high density (HD, 120 g/m³) for 90 days. At the end of the experiment, fish reared in the MD and HD groups showed lower growth performance than those from the LD group. The HD treatment significantly altered the physiological parameters, including glucose and lactate. Meanwhile, the HD treatment induced oxidative stress and lipid peroxidation after 90 days of farming. Furthermore, transcriptomic analysis revealed that HD treatment led to abnormal lipid metabolism. Interestingly, we found the suppression of three key pathways related to lipid metabolism, including the PPAR, insulin and adipocytokine signaling pathways, in the HD group. Overall, our data indicated that the HD treatment inhibited growth and caused physiological responses, oxidative stress and abnormal hepatic lipid metabolism in M. salmoides in an integrated rice–fish farming system.