Integrated physiological, transcriptomic, and metabolomic analyses provide new insights into hypoxia tolerance in large yellow croaker (Larimichthys crocea).

Integrated Transcriptomic and Metabolomic Analysis Reveals the Regulatory Mechanisms of Macrobrachium rosenbergii in Response to Acute High-Salinity Stress

Simple Summary Macrobrachium rosenbergii is an economically important species in freshwater aquaculture. However, climate change and rising sea levels are causing sudden increases in salt levels in farming areas, threatening their survival and regional economies. This study aimed to understand the internal survival strategies of adult prawns when exposed to sudden high salt conditions over a two-day period. By examining the active genes and metabolites in the prawns, researchers discovered that the animals shift from a quick stress response to a systemic physical adjustment. The results showed that to survive the salty environment, the prawns activate internal cell cleaning and repair systems while changing how they use fats and energy. Most importantly, they use a unique strategy to reduce the breakdown of specific amino acids, retaining these molecules to balance the intense outside salt pressure. In conclusion, these prawns survive extreme salt stress by combining cellular protection with a metabolite saving strategy. This research not only decodes the survival mechanisms of these prawns but also provides a basis for breeding salt-resistant varieties, helping the aquaculture industry better address the practical challenges posed by climate change.

Physiological, Transcriptomic, and Metabolomic Insights into Ammonia-Nitrogen Stress in the Hepatopancreas of Litopenaeus vannamei Acclimated to Low Salinity

Simple Summary Low-salinity farming is popular for Litopenaeus vannamei cultivation but easily causes ammonia accumulation that endangers shrimp survival. Most previous studies focus on single stress or normal salinity, while the shrimp response to ammonia stress after low-salinity adaptation remains unclear. Here, we acclimated shrimp to 5‰ salinity and exposed them to high ammonia for 96 h. Ammonia stress caused hepatopancreatic oxidative damage and disturbed hemolymph nitrogen metabolism. Multi-omics analysis revealed 112 differentially expressed genes (DEGs) and altered lipid and amino acid metabolism. Three core secretion, metabolism and immune pathways, together with key gene-metabolite pairs, were identified. This study clarifies the physiological and molecular mechanisms underlying shrimp tolerance to combined low-salinity and ammonia stress, supporting the healthy development of low-salinity aquaculture.

Transcriptomic insights into renal osmoregulation and environmental adaptation in two hammerhead shark species (Sphyrna zygaena and Sphyrna lewini)

Multi-omics analysis provides new insights into the adaptive strategies of Procambarus clarkii in response to acute hypoxia stress

Suitable dissolved oxygen levels are crucial for crustacean respiration and energy metabolism. To investigate the molecular mechanisms underlying hypoxia adaptation in the red swamp crayfish ( Procambarus clarkii ), we performed an integrated multi-omics analysis combining RNA-Seq transcriptomics and LC-MS non-targeted metabolomics on gill tissues under acute hypoxic (2.0±0.2 mg/L) and normoxic (7.5±0.2 mg/L) conditions. A total of 1,021 differentially expressed genes (DEGs) and 286 differentially expressed metabolites (DEMs) were identified. KEGG enrichment analysis revealed that DEGs were predominantly associated with lipid metabolism pathways, whereas DEMs were significantly enriched in nucleotide metabolism, purine metabolism, ABC transporter pathways and unsaturated fatty acid biosynthesis. Integrated transcriptomic and metabolomic analysis revealed 47 genes and 47 metabolites significantly associated across multiple key metabolic pathways, including lipid, carbohydrate, amino acid, and nucleotide metabolism. Specifically, genes associated with lipid synthesis and lipid degradation were upregulated, while the pentose phosphate pathway was activated to provide raw materials for fatty acid synthesis and produce NADPH to defend cell membranes from oxidative stress damage, indicating significant adjustments in energy metabolism pathways under hypoxic conditions. These findings provide a theoretical basis for deepening our understanding of hypoxic adaptation strategies in crustaceans. This multi-omics integration systematically revealed a coordinated metabolic reprogramming strategy in the gills of P. clarkii under acute hypoxia. These findings highlight the shift toward enhanced lipid turnover and NADPH production pathways (e.g., the pentose phosphate pathway) as key adaptive mechanisms, providing new insights into energy homeostasis and hypoxia tolerance in crustaceans beyond the traditional glycolysis-centered model.

Transcriptomic insights into exogenous fatty acid-enhanced halotolerance in Zygosaccharomyces rouxii.

BACKGROUND High salinity restricts microbial growth during brine-based food fermentation. Although exogenous unsaturated fatty acids improve the salt tolerance of Zygosaccharomyces rouxii, the associated transcriptional mechanisms remain unclear. This study investigated the transcriptomic response of Z. rouxii CGMCC 3791 to palmitoleic acid (C16:1) under high salt conditions. RESULTS Cells were cultured in yeast extract peptone dextrose (YPD) containing 120 g L-1 NaCl, with or without 20 μg mL-1 C16:1. They were analyzed by RNA sequencing. Principal component analysis clearly separated the two treatments. Using q < 0.05 and |log2 fold change| > 1, 23 differentially expressed genes were identified - three upregulated and 20 downregulated. INO1, MLS1, POX1, MEP2, and SOD5 were among the major responsive genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that peroxisome-associated functions, lipid metabolism, oxidative stress responses, nitrogen utilization, and mitogen-activated protein kinase (MAPK) signaling were the principal C16:1-responsive processes. CONCLUSION Exogenous C16:1 elicited a focused transcriptional adjustment rather than broad transcriptome-wide reprogramming in salt-stressed Z. rouxii. The results indicated that peroxisome-linked lipid processes and redox regulation were candidate mechanisms underlying fatty-acid-associated halotolerance and provided targets for improving the robustness of high-salt food fermentation. © 2026 Society of Chemical Industry.

Integrated Physiological, Transcriptomic, and Metabolomic Analyses Reveal the Mechanism Underlying the Response of Alfalfa to Combined Salt and Heat Stress.

Combined stress more strongly inhibited plant height, stem diameter, fresh weight, net photosynthetic rate, and transpiration rate than single stresses, and insights into alfalfa adaptation to multiple abiotic stresses are provided.