Transcriptome analysis of hepatopancreas in penaeus monodon under acute low pH stress

Integrated microbiome and metabolome analyses reveal the effects of low pH on intestinal health and homeostasis of crayfish (Procambarus clarkii)

Low pH (LpH) poses a significant challenge to the health, immune response, and growth of aquatic animals worldwide. Crayfish (Procambarus clarkii) is a globally farmed freshwater species with a remarkable adaptability to various environmental stressors. However, the effects of LpH stress on the microbiota and host metabolism in crayfish intestines remain poorly understood. In this study, integrated analyses of antioxidant enzyme activity, histopathological damage, 16S rRNA gene sequencing, and liquid chromatography-mass spectrometry (LC-MS) were performed to investigate the physiology, histopathology, microbiota, and metabolite changes in crayfish intestines exposed to LpH treatment. The results showed that LpH stress induced obvious changes in superoxide dismutase and catalase activities and histopathological alterations in crayfish intestines. Furthermore, 16S rRNA gene sequencing analysis revealed that exposure to LpH caused significant alterations in the diversity and composition of the crayfish intestinal microbiota at the phylum and genus levels. At the genus level, 14 genera including Bacilloplasma, Citrobacter, Shewanella, Vibrio, RsaHf231, Erysipelatoclostridium, Anaerorhabdus, Dysgonomonas, Flavobacterium, Tyzzerella, Brachymonas, Muribaculaceae, Propionivibrio, and Comamonas, exhibited significant differences in their relative abundances. The LC-MS analysis revealed 859 differentially expressed metabolites in crayfish intestines in response to LpH, including 363 and 496 upregulated and downregulated metabolites, respectively. These identified metabolites exhibited significant enrichment in 24 Kyoto Encyclopedia of Genes and Genomes pathways (p < 0.05), including seven and 17 upregulated and downregulated pathways, respectively. These pathways are mainly associated with energy and amino acid metabolism. Correlation analysis revealed a strong correlation between the metabolites and intestinal microbiota of crayfish during LpH treatment. These findings suggest that LpH may induce significant oxidative stress, intestinal tissue damage, disruption of intestinal microbiota homeostasis, and alterations in the metabolism in crayfish. These findings provide valuable insights into how the microbial and metabolic processes of crayfish intestines respond to LpH stress.

Effects of miR-722 on gene expression and alternative splicing in the liver of half-smooth tongue sole after infection with Vibrio anguillarum

MicroRNAs play crucial roles in various biological processes, including but not limited to differentiation, development, disease, and immunity. However, their immunoregulatory roles in half-smooth tongue sole are lacking. Our previous studies indicated that miR-722 could target C5aR1 to modulate the complement pathway to alleviate inflammatory response and even affect the mortality after the bacterial infection with Vibrio anguillarum. Driven by the purpose of revealing the underlying mechanisms, in this study, we investigated the effects of miR-722 on the gene expression and alternative splicing (AS) in the liver of half-smooth tongue sole after Vibrio anguillarum infection, with the approach of miR-722 overexpression/silencing and subsequent RNA-seq. Among the different comparisons, the I group (miR-722 inhibitor and V. anguillarum) versus blank control (PBS) exhibited the highest number of differentially expressed genes (DEGs), suggesting that the immune response was overactivated after inhibiting the miR-722. In addition, enrichment analyses were performed to reveal the functions of DEGs and differential AS (DAS) genes, reflecting the enrichment of RNA splicing and immune-related pathways including NF-κB and T cell receptor signaling pathway. Comparing the M group (miR-722 mimic and V. anguillarum) with the negative control (random sequence and V. anguillarum), two immune-related genes, cd48 and mapk8, were differentially expressed, of which mapk8 was also differentially spliced, indicating their importance in the immune response. Furthermore, representative gene analysis was performed, suggesting their corresponding functional changes due to AS. To verify the RNA-seq data, quantitative real-time PCR was employed with twenty pairs of primers for DEGs and DAS events. Overall, our results demonstrated that miR-722 could mediate the transcriptome-wide changes of gene expression and AS in half-smooth tongue sole, and provided insights into the regulatory role of miR-722 in immune responses, laying the foundation for further functional analyses and practical applications in aquaculture.

Stress responses to warming in Japanese flounder (Paralichthys olivaceus) from different environmental scenarios

Japanese flounder (Paralichthys olivaceus) is one of cold-water species widely farmed in Asia. In recent years, the increased frequency of extreme weather events caused by global warming has led to serious impact on Japanese flounder. Therefore, it is crucial to understand the effects of representative coastal economic fish under increasing water temperature. In this study, we investigated the histological and apoptosis responses, oxidative stress and transcriptomic profile in the liver of Japanese flounder exposed to gradual temperature rise (GTR) and abrupt temperature rise (ATR). The histological results showed liver cells in ATR group were the most serious in all three groups including vacuolar degeneration and inflammatory infiltration, and had more apoptosis cells than GTR group detected by TUNEL staining. These further indicated ATR stress caused more severe damage than GTR stress. Compared with control group, the biochemical analysis showed significantly changes in two kinds of heat stress, including GPT, GOT and D-Glc in serum, ATPase, Glycogen, TG, TC, ROS, SOD and CAT in liver. In addition, the RNA-Seq was used to analyze the response mechanism in Japanese flounder liver after heat stress. A total of 313 and 644 differentially expressed genes (DEGs) were identified in GTR and ATR groups, respectively. Further pathway enrichment of these DEGs revealed that heat stress affected cell cycle, protein processing and transportation, DNA replication and other biological processes. Notably, protein processing pathway in the endoplasmic reticulum (ER) was enriched significantly in KEGG and GSEA enrichment analysis, and the expression of ATF4 and JNK was significantly up-regulated in both GTR and ATR groups, while CHOP and TRAF2 were high expressed in GTR and ATR groups, respectively. In conclusion, heat stress could cause tissue damage, inflammation, oxidative stress and ER stress in the liver of Japanese flounder. The present study would provide insight into the reference for the adaptive mechanisms of economic fish in face of increasing water temperature caused by global warming.

Transcriptome analysis of digestive diverticula of Hong Kong oyster (Crassostrea hongkongesis) infected with Vibrio harveyi

The Hong Kong oyster (Crassostrea hongkongesis), as the main marine aquaculture shellfish in the South China Sea, not only has high economic and ecological value, but also is an ideal model for conducting research on pathogen host interaction. However, diseases caused by Vibrio pose a serious impediment to the culture of C. hongkongesis. In this study, we performed transcriptome analysis of digestive diverticula of C. hongkongesis infected with V. harveyi. A total of 977, 689, 912 high quality reads and 955, 208, 562 valid reads were obtained. At 12, 24, 48 and 72 h post-infection, 1402, 2168, 2727 and 1398 differentially expressed genes (DEGs) were captured, respectively. GO enrichment analysis showed that DEGs were significantly enriched in cellular processes, catalytic activity, cell part and other terms. KEGG enrichment analysis revealed that these DEGs were mainly closely related to Necroptosis, RIG-I-like receptor signaling pathway, NF-kappa B signaling pathway, Toll-like receptor signaling pathway and other pathways are related. The results of WGCNA analysis indicated that THBS1, CA10, Trpm2, THAP12, PTPRT, HSPA12A, and ADAM10 were the hub genes in the gene co-expression network. This study will provide new ideas at the transcriptome level for the immune regulatory mechanisms and adaptability of the C. hongkongesis to V. infection, as well as for achieving selective breeding for Vibrio resistance in the C. hongkongesis.

Changes in pH and Nitrite Nitrogen Induces an Imbalance in the Oxidative Defenses of the Spotted Babylon (Babylonia areolata)

In order to reveal the acute toxicity and physiological changes of the spotted babylon (Babylonia areolata) in response to environmental manipulation, the spotted babylon was exposed to three pH levels (7.0, 8.0 and 9.0) of seawater and four concentrations of nitrite nitrogen (0.02, 2.7, 13.5 and 27 mg/L). The activities of six immunoenzymes, superoxide dismutase (SOD), glutathione peroxidase (GSH-PX), catalase (CAT), acid phosphatase (ACP), alkaline phosphatase (AKP) and peroxidase (POD), were measured. The levels of pH and nitrite nitrogen concentrations significantly impacted immunoenzyme activity over time. After the acute stress of pH and nitrite nitrogen, the spotted babylon appeared to be unresponsive to external stimuli, exhibited decreased vigor, slowly climbed the wall, sank to the tank and could not stand upright. As time elapsed, with the extension of time, the spotted babylon showed a trend of increasing and then decreasing ACP, AKP, CAT and SOD activities in order to adapt to the mutated environment and improve its immunity. In contrast, POD and GSH-PX activities showed a decrease followed by an increase with time. This study explored the tolerance range of the spotted babylon to pH, nitrite nitrogen, and time, proving that external stimuli activate the body's immune response. The body's immune function has a specific range of adaptation to the environment over time. Once the body's immune system was insufficient to adapt to this range, the immune system collapsed and the snail gradually died off. This study has discovered the suitable pH and nitrite nitrogen ranges for the culture of the spotted babylon, and provides useful information on the response of the snail's immune system.