Quantity, function, and quality: A stepwise mitochondrial strategy underpins hypoxia adaptation in Apostichopus japonicus elucidated by phenotypic, proteomic, and metabolomic analysis

Dissolved oxygen (DO) is a key factor in aquatic ecosystems, and its fluctuation—driven by climate change and human activity—poses increasing stress on marine organisms. Here, we investigated the mitochondrial responses of the sea cucumber Apostichopus japonicus to varying DO levels (7, 4, and 2 mg/L) using phenotypic, proteomic, and metabolomic analyses. Structural observations revealed increased cristae density at 4 mg/L and mitochondrial swelling and fragmentation at 2 mg/L. Hypoxic conditions reduced membrane potential and ATP production while increasing H2O2 levels. Mitochondrial copy number rose under moderate hypoxia but declined under severe hypoxia. Proteomic analysis (DIA-MS) identified 1,307 and 2,042 differentially expressed proteins in DO4 vs DO7 and DO2 vs DO7, respectively, which were enriched in pathways such as fatty acid metabolism and glycolysis. Metabolomic profiling (LC-MS/MS) detected 238 and 219 differential metabolites in the same comparisons, linked to sulfur and amino acid metabolism. Integrated analysis revealed that A. japonicus mitochondria adapt to hypoxia via a stepwise strategy involving quantity regulation, functional optimization, and quality control, which are achieved through modifications in mitochondrial dynamics, energy metabolism, oxidative stress, autophagy, and apoptosis. This study provides a valuable multi-omic dataset capturing mitochondrial responses to environmental oxygen variability in a non-model marine species. This comprehensive study lays a foundation for understanding the oxygen adaptation mechanisms of benthic echinoderms and facilitates broader molecular ecology research in the context of changing marine environmental conditions.