Multi-Tissue Transcriptomics Analysis of the Effects of Ammonia Nitrogen Stress on Metabolism, Immunity, and Comprehensive Stress Responses in Megalobrama amblycephala

In order to reveal the molecular response characteristics of different tissues of Megalobrama amblycephala under ammonia nitrogen stress, the liver, gill, muscle, kidney and brain tissues of juvenile Megalobrama amblycephala (12.05 ± 0.04 g) under 25 mg/L ammonium chloride stress were used as the research objects. The transcriptome sequencing technology was used to systematically analyze the transcriptional expression changes. A total of 204.42 Gb transcription data were obtained, and a total of 3039 DEGs were detected, of which 1331 genes were up-regulated and 1708 genes were down-regulated. Ten DEGs were randomly selected for quantitative qRT-PCR analysis, and the results confirmed that the transcriptome results were reliable. Multi-organ synergy analysis suggested that overlapping DEGs (e.g., ZNF239, DMBT1, NLRC3, MHC-I, and CCL8) may exhibit similar or opposing regulatory patterns across organs, potentially reflecting complementary and coordinated mechanisms in immune regulation, inflammatory responses, energy allocation, and detoxification strategies among organ systems. GO and KEGG pathway enrichment analysis of differentially expressed genes showed that ammonia nitrogen mainly affected immune inflammation-related processes, material transport and degradation, protein homeostasis maintenance, oxidative stress defense, membrane lipid metabolism remodeling, and energy metabolism regulation. In different tissues, genes related to specific functions are enriched according to their physiological roles: in the liver, genes related to detoxification and damage clearance are enriched; in the gill, genes related to barrier defense and antioxidant/detoxification are enriched; in the kidney, genes related to damage response and metabolic regulation are enriched; in the brain, genes related to membrane lipid homeostasis and protective stress are enriched; and in the muscle, genes related to energy metabolism and structural function adjustment are enriched. This study elucidated the multi-tissue response characteristics of Megalobrama amblycephala under ammonia nitrogen stress at the transcriptome level, providing fundamental data and references for further clarifying the mechanisms of ammonia nitrogen toxicity in fish and screening stress-responsive marker genes.