Integrative analysis of transcriptomics and gut microbiome in grass carp under alkalinity stress

Alkalinity, a key environmental stressor in saline-alkali ecosystems, adversely affects the growth and survival of aquatic organisms. Genetic improvement of alkali-tolerant fish strains offers a promising strategy for utilizing saline-alkaline water resources; however, the molecular mechanisms underlying the response to alkalinity stress remain inadequately understood. This study aimed to identify novel molecular signatures of alkaline exposure in grass carp by integrating gut microbiome profiling with host transcriptome data. Histological analysis revealed significant alterations in the height of intestinal folds, muscle layer thickness, and fold width in response to NaHCO₃ exposure, along with an increased number of goblet cells under alkalinity stress. Differential gene expression (DEGs) analysis identified 1620, 6564, and 3190 genes with significant expression changes at 24, 48, and 72 h of NaHCO₃ treatment, respectively, compared to controls. Several known alkalinity-responsive genes, such as aquaporin 1a (aqp1a), carbonic anhydrase 6 (ca6), heat shock protein 30 (hsp30), prostaglandin-endoperoxide synthase 2b (ptgs2b), caspase 23 (casp23), solute carrier family 7a (slc7a), toll-like receptor 5 (tlr5), and toll-like receptor 13 (tlr13), were identified and validated through real-time quantitative PCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that immune- and disease-related signaling pathways played critical roles in mitigating acute alkaline stress. Furthermore, a total of 1,521,323 quality-filtered sequences with an average of 416 bp in length were generated through 16S rRNA sequencing. Bioinformatics analysis indicated that NaHCO₃ exposure reduced microbial diversity and altered the gut microbiota composition in grass carp. Notably, Fusobacteriota abundance significantly increased, while Firmicutes and Proteobacteria decreased substantially at 48 h post-alkalinity stress. Integrative analysis further highlighted strong correlations between specific bacterial taxa and alkalinity-responsive differentially expressed genes (DEGs). These findings provided valuable insights into the molecular mechanisms underlying alkalinity stress and identified potential targets for molecular breeding to enhance alkaline tolerance in grass carp.