Integration of transcriptomic and metabolomic reveals carbonate alkalinity stress responses in the hepatopancreas of Litopenaeus vannamei

Integration of microbiomics and metabolomics reveals energy metabolism imbalance in crucian carp (Carassius auratus) under saline-alkaline exposure

The ecological conditions of freshwater aquaculture are deteriorating by degrees in recent years. Consequently, the comprehensive utilization of saline-alkaline water has garnered increasing societal attention. Here, crucian carp (Carassius auratus) were exposed to 20, 40 mmol/L NaHCO3 for 30 days (T, F group). Metabolomic analyses were conducted using UPLC-QTOF/MS, complemented by biochemical and microbiology profiling to elucidate the damage of the saline environment to the intestinal microbial structure, which in turn interfered with the energy metabolism. It was observed that carbonate alkalinity (CA) exposure not only caused intestine oxidative stress but also changed the levels of several digestive enzymes, including α-amylase (AMS), chymotrypsin (CHY), lipase (LPS). Metabolomic analysis identified 22 different metabolites (DEMs) in T group and 77 DEMs in F group. MetaboAnalyst analysis indicated that these metabolites are primarily involved in energy-related pathways, including the citric acid cycle, galactose metabolism, and glycine, serine, and threonine metabolism. Intestinal microbial diversity and community composition were altered under carbonate alkalinity exposure, with increase in Proteobacteria abundance and decline in Firmicutes, abundance alongside enrichment of Sphingomonas. Herein, saline-alkaline stress disrupted the physiological homeostasis of the crucian carp intestine, leading to microbial dysbiosis and energy metabolic imbalance. This study provides a theoretical foundation for understanding the stress response of the crucian carp intestine and the role of the intestinal microbiome in host resilience under adverse environmental conditions.

Genetic Diversity and Population Structure of Macrobrachium nipponense Populations in the Saline-Alkaline Regions of China

The oriental river prawn Macrobrachium nipponense is of great economic importance in China. However, its culture in the saline-alkaline regions is limited. This study used D-loop region sequences to analyze the genetic diversity and population structure across the saline-alkaline regions of China. A total of 264 individuals were successfully sequenced from nine sites, including Daqing in Heilongjiang Province (HLJ), Songyuan in Jilin Province (JL), Ulanhot in the east of inner Mongolia (NMG), Jingtai in Gansu Province (GS), Dongying in Shandong Province (SD), Dongtai in Jiangsu Province (JS), Nanchang in Jiangxi province (JX), Tianjin in mainland China (TJ), and Yinchuan in Ningxia Province (NX). In addition, 89 haplotypes were defined. The haplotype diversity (h) and nucleotide diversity π showed remarkable genetic diversity in the JS, NX, JL, and TJ sites. It was found that the genetic variation within sites was relatively greater. The genetic distance (D) and the pairwise genetic differentiation index (FST) revealed that SD and GS are closely related. The FST values among the nine sites were significant except for the one between SD and HLJ (p-value > 0.05). The cluster analyses and the phylogenetic tree identified two main groups. There is an association among sites by geographic location, and the JS site shows higher diversity. The results of this study provide basic information for the protection and development of M. nipponense resources in the saline-alkaline regions of China.

Study on the physiological responses and tolerance mechanisms to subchronic carbonate alkalinity exposure in the gills of Paramisgurnus dabryanus

Given the reduction of freshwater resources, saline-alkaline aquaculture has emerged as an effective approach to expand the fishery's accessible space. High carbonate alkalinity (CA) is a major stressor for aquatic organisms in saline-alkaline environments. Paramisgurnus dabryanus is a potential species for culture in saline-alkaline water, making it an ideal model for investigating the physiological responses and tolerance mechanisms to CA exposure in freshwater fishes. In the current study, P. dabryanus were exposed to 15 and 30 mmol/L NaHCO3, combining blood biochemical, gill histological, transcriptomic, and metabolomic methods for conjoint analysis of response mechanisms. After 28-d exposure, the gill ventilation frequency of P. dabryanus decreased significantly, gill lamellae twisted and atrophied, and gill filament epithelial cells proliferated, potentially limiting gas exchange, whereas the accessory air-breathing frequency increased significantly, possibly for greater oxygen uptake. Serum osmolality and blood pH remained relatively steady, while serum ammonia levels rose significantly. A total of 3718 differentially expressed genes (DEGs) and 205 differential metabolites (DMs) were identified between the control group and 30 mmol/L NaHCO3 group, involved in ion transport (Na+/K+-ATPase, V-type ATPase, carbonic anhydrase, and ABC transporters), ammonia transport (Rh glycoproteins and Aquaporins), amino acid metabolism, carbohydrate metabolism, and fatty acid metabolism. Furthermore, DEGs were significantly associated with cell-cell/ extracellular matrix interaction and protein synthesis. An integrated multi-omics analysis revealed the activation of carbon metabolism and TCA cycle. These results indicate that in response to CA exposure, P. dabryanus may facilitate carrier-mediated ion and ammonia transport to maintain the internal osmotic equilibrium and lessen the deleterious effects of blocked ammonia excretion. Meanwhile, amino acid metabolism and protein synthesis are disturbed, P. dabryanus can modulate carbohydrate catabolism to maintain energy homeostasis. The above findings provide novel insights into saline-alkaline adaptation in freshwater fishes, paving the way for future research and development of saline-alkaline-tolerant Cobitidae strains.

Integrated analysis of transcriptome and metabolome reveals chronic low salinity stress responses in the muscle of Exopalaemon carinicauda

Low salinity environment is one of the key factors threatening the survival of aquatic organisms. Due to the strong adaptability of low salinity, Exopalaemon carinicauda is an ideal model to study the low salinity adaptation mechanism of crustaceans. In this study, E. carinicauda from the same family were divided into two groups, which were reared at salinity of 4 ‰ and 30 ‰, respectively. Integrated analysis of transcriptome and metabolome was used to uncover the mechanisms of E. carinicauda adaptation to chronic low salinity environment. Under the chronic low salinity stress, a total of 651 differentially expressed genes (DEGs) and 386 differential metabolites (DMs) were obtained, with the majority showing downregulation. These DEGs mainly involved MAPK signal transduction pathway and structural constituent of cuticle. Besides, chitin binding and chitin metabolism process were inhibited significantly. Among the DMs, lipids and lipid-like molecules, flavor amino acids and nucleotides were detected, which may be related to the adjustment of energy metabolism and flavor of muscle. In addition, ubiquinone and other terpenoid-quinone biosynthesis pathway and alanine, aspartate, and glutamate metabolic pathway were induced. These results will enrich our understanding of the molecular mechanism underlying the chronic low salinity tolerance in E. carinicauda, providing an important theoretical basis and practical guidance for the research and breeding, thereby promoting the sustainable development of aquaculture.

LC-MS untargeted metabolomics reveals metabolic disturbance and ferroptosis in MWCNTs-induced hepatotoxicity of Cyprinus carpio

In recent years, there is a great concern about the potential adverse effects of carbon nanotubes (CNTs) on the aquatic systems due to their increasingly extensive application. In this study, juvenile Cyprinus carpio were exposed to multi-walled CNTs (MWCNTs) at concentrations of 0, 0.25, and 2.5 mg L-1 for 28 days. Then, oxidative stress indicators and metabolite profile of the livers were assessed. Results showed the significant increase of malondialdehyde (MDA) content and decrease of glutathione (GSH) activities in fish treated with 2.5 mg L-1 MWCNTs. LC-MS untargeted metabolomics demonstrated that 406 and 274 metabolites in fish treated with 2.5 mg L-1 MWCNTs were significantly up- and down-regulated, respectively. KEGG functional annotation analysis showed the disturbance of amino acid metabolism, lipid metabolism, and nucleotide metabolism. In addition, ferroptosis signaling pathway was detected. Therefore, iron content analysis and quantitative real-time RT-PCR assay were performed furtherly to validate the contribution of ferroptosis to MWCNTs-induced hepatotoxicity. The iron content increased significantly and the mRNA levels of ferroptosis-related genes including STEAP3, ACSL4, NCOA4, TFR1, NRF2, SLC3A2, SLC7A11, GPX4, and FPN1 were also obviously changed. Taken together, our study suggested that MWCNTs exposure-induced ferroptosis were associated with iron overload and lipid peroxidation via NRF2/SLC7A11/GSH/GPX4 axis. Our findings provide essential information to understand the mechanism of CNTs-induced hepatotoxicity in fish and explore potential biomarkers.

Physiological Adaptation of Fenneropenaeus chinensis in Response to Saline-Alkaline Stress Revealed by a Combined Proteomics and Metabolomics Method

The rapid development of the mariculture industry has been hindered by limited coastal aquaculture space. To utilize the abundant inland saline-alkaline water, we studied the physiological effects of high carbonate alkalinity stress and high pH stress on Fenneropenaeus chinensis. The study employed quantitative proteomics by tandem mass tag (TMT) and non-targeted metabolomics analysis using a liquid chromatograph mass spectrometer (LC-MS) to understand the physiological and biochemical adaptive mechanisms of the hepatopancreas of F. chinensis in response to saline-alkaline stress at the molecular level. We designed two stress groups as follows: a high carbonate alkalinity (CA) group and a combined high carbonate alkalinity and high pH (CP) group. The study found that the protein and metabolic profiles of the two stress groups were changed, and the CP group, which was exposed to dual stresses, incurred more severe damage to the hepatopancreas compared to that of the CA group. After exposure to CA and CP, the hepatopancreas of F. chinensis showed significant alterations in 455 proteins and 50 metabolites, and 1988 proteins and 272 metabolites, respectively. In addition, F. chinensis upregulated the level of energy metabolism in the hepatopancreas to defend against osmotic imbalance caused by CA or CP stress, which was demonstrated by the significant upregulation of important proteins and metabolites in glycolysis, pyruvate metabolism, TCA cycle, and fatty acid oxidation. Additionally, pattern recognition receptors, the phenol oxidase system, and various immune-related metabolic enzymes and metabolites were also affected. The immune homeostasis of F. chinensis was affected by the alteration of the antioxidant system following exposure to CA or CP. These findings provide valuable information for F. chinensis saline-alkaline water cultivation practices.

The toxic effects of tetracycline exposure on the physiological homeostasis of the gut-liver axis in grouper

Antibiotic residues, such as tetracycline (TET), in aquatic environments have become a global concern. The liver and gut are important for immunity and metabolism in aquatic organisms. In this study, juvenile groupers were subjected to 1 and 100 μg/L TET for 14 days, and the physiological changes of these fish were evaluated from the perspective of gut-liver axis. After TET exposure, the liver showed histopathology, lipid accumulation, and the elevated ALT activity. An oxidative stress response was induced in the liver and the metabolic pattern was disturbed, especially pyrimidine metabolism. Further, intestinal health was also affected, including the damaged intestinal mucosa, the decreased mRNA expression levels of tight junction proteins (ZO-1, Occludin, and Claudin-3), along with the increased gene expression levels of inflammation (IL-1β, IL-8, TNF-α) and apoptosis (Casp-3 and p53). The diversity of intestinal microbes increased and the community composition was altered, and several beneficial bacteria (Lactobacillus, Bacteroidales S24-7 group, and Romboutsia) and harmful (Aeromonas, Flavobacterium, and Nautella) exhibited notable correlations with hepatic physiological indicators and metabolites. These results suggested that TET exposure can adversely affect the physiological homeostasis of groupers through the gut-liver axis.

Effects of Tannin Supplementation in Diet on the Resistance to Ammonia Stress of Pacific White Shrimp Litopenaeus vannamei

Tannin (TA), as a natural phenolic compound with strong antioxidant activity, has been used as a feed additive for various animals. In this study, we fed a diet containing 800 mg/kg of tannin on Litopenaeus vannamei for 56 days and then subjected to acute ammonia stress for 48 hr to investigate the effect of dietary tannin on the ammonia stress response of L. vannamei through transcriptomic and metabolomic analysis. The transcriptome analysis indicated that ammonia stress-induced differential expression of 4,185 genes, while tannin-fed shrimp only had 964 differentially expressed genes. Compared with the TA_0 group, 59 pathways were significantly altered, and the pathways of "starch and sucrose metabolism," "retinol metabolism," "arachidonic acid metabolism," "lysosome," and "amino sugar and nucleotide sugar metabolism" were highly enriched in the TS_0 group. Compared with the TS_0 group, six pathways were significantly altered, and the pathways of "dilated cardiomyopathy," "complement and coagulation cascades," "cardiac muscle contraction," "fructose and mannose metabolism," "cGMP-PKG signaling pathway," and "beta-alanine metabolism" were significantly enriched in the TS_800 group. Metabolomic analysis showed that a total of 107 differential metabolites (DMs) were identified in the TS_0 vs. TA_0 group, while 75 DMs were identified in the TS_800 vs. TS_0 group. Based on KEGG annotation, it was found that a large amount of DM was significantly enriched in amino acid metabolism pathways in the TS_0 group, including "arginine and proline metabolism," "alanine, aspartic acid, and glutamic acid metabolism," "β-Alanine metabolism and tyrosine metabolism" indicated that tannins affect the metabolism of amino acids. The integration of DEGs and DMs indicates that dietary tannins highly alter the digestion and absorption functions of proteins, as well as the biosynthesis and metabolism of amino acids. This study provides new insights into the adaptation of Pacific white shrimp to ammonia stress and the addition of tannins to feed to enhance immune function.

Integrated characterizations of intestinal bacteria and transcriptomics revealed the acute stress response to carbonate alkalinity in white shrimp Penaeusvannamei

The impact of carbonate alkalinity in saline-alkaline water on aquatic organisms, particularly Penaeus vannamei, a significant species in aquaculture, remains a critical area of study. To elucidate the acute response mechanisms of P. vannamei to elevated carbonate alkalinity environments, we utilized 16S rRNA gene and transcriptome sequencing technologies to analyze intestinal bacteria and gene expressions within various tissues. Our investigation revealed notable changes in specific intestinal bacterial OTUs, whose abundances varied preceding the overall bacterial community, indicating the sensitivity to carbonate alkalinity exposure. These shifts are accompanied by a simplification in bacterial networks and alterations in pathogenic OTUs, notably Aeromonas OTU. Concurrently, gene expression variations were observed across the hepatopancreas, gills, muscles, and intestines, with decreasing numbers of DEGs in the mentioned order. Annotation of these DEGs revealed enrichments in pathways related to transport, catabolism, immune responses, circulatory functions, and lipid metabolism. Notably, correlations between specific intestinal bacterial OTUs and gene expression shifts were identified across these tissues. Several OTUs, attributed to Rhizobiales, Saccharimonadales, Acidovora, and Aeromona, exhibited a correlation with DEGs in all four tissues, primarily associated with amino acid metabolism, signal transduction, and transport and catabolism pathways. Our study provides comprehensive insights into the dynamic responses of P. vannamei to elevated carbonate alkalinity stress. These findings contribute crucial knowledge for effective P. vannamei cultivation in saline-alkaline water, advancing our understanding in this field.

Metabolomic responses based on transcriptome of the hepatopancreas in Exopalaemon carinicauda under carbonate alkalinity stress

High carbonate alkalinity is one of the major stress factors for survival of aquatic animals in saline-alkaline water. Exopalaemon carinicauda is a good model for studying the saline-alkaline adaption mechanism in crustacean because of its great adaptive capacity to alkalinity stress. In this study, non-targeted liquid chromatography-mass spectrometry (LC-MS) metabolomics analyses based on high-throughput RNA sequencing (RNA-Seq) were used to study the metabolomic responses of hepatopancreas in E. carinicauda at 12 h and 36 h after acute carbonate alkalinity stress. The results revealed that most of the significantly differential metabolites were related to the lipid metabolism. In particular, the sphingolipid metabolism was observed at 12 h, the glycerophospholipid metabolism was detected at 36 h, and the linoleic acid metabolic pathway was significantly enriched at both 12 h and 36 h. The combined transcriptome and metabolome analysis showed that energy consumption increased at 12 h, resulting in significant enrichment of AMPK signaling pathways, which contributed to maintain energy homeostasis. Subsequently, the hepatopancreas provided sufficient energy supply through cAMP signaling pathway and glycerophosphate metabolism to maintain normal metabolic function at 36 h. These findings might help to understand the molecular mechanisms of the E. carinicauda under carbonate alkalinity stress, thereby promote the research and development of saline-alkaline resistant shrimp.