Adapting under Hypoxia: Cellular Heterogeneity and Metabolic Plasticity of Estuarine Oysters in Fluctuating Environments

Abstract Coastal oxygen depletion occurs as sustained hypoxia, oxygen cycling, and near-anoxic events, yet assessments often rely on constant dissolved oxygen and ignore fluctuating exposure patterns. Whether these distinct oxygen depletion regimes induce different cellular and metabolic configurations in intertidal organisms remains to be determined. Here, we exposed estuarine oysters to three ecologically relevant oxygen depletion regimes and profiled the gill transcriptomes at single-cell resolution. Across three hypoxia modes, gills converged on a shared program by constrained energy budgeting, broad suppression of proliferation, and shifts in inferred fate programs, consistent with reduced turnover and increased reliance on state transitions. High-dimensional weighted gene coexpression network analysis (hdWGCNA) condensed hypoxia responses into two conserved coexpression modules, including a cytoprotective tolerance program enriched for proteostasis, mitochondrial maintenance and negative regulation of cell death, and a detoxification and cytoskeletal remodeling program enriched for glutathione-linked redox handling and structural dynamics. Inference of intercellular communication indicated that hypoxia altered the communication weight and number while preserving neuroendocrine cells (NECs) as stable hubs. On this shared foundation, exposure patterns produced specific strategies for sensitive cell units. Consistent hypoxia preferentially allocated ionocytes and replacement for the subcluster to maintain homeostasis, along with immune clearance and tissue maintenance. Oxygen cycling coordinated phagocyte effectors with sentinel epithelial alarm amplification to resist repeated reactive oxygen species (ROS) burden. Anoxia reinforced mucosal and humoral defenses under systemic constraints. Overall, this study provides a single-cell transcriptomic framework for understanding how cellular heterogeneity and metabolic plasticity in a key interface organ enabled estuarine oysters to adapt to diverse and fluctuating hypoxic environments.