Insights into enhanced, divergent, and additive responses to single and combined hypoxia-salt stress

Plants frequently encounter simultaneous stressors, requiring complex adaptive responses across regulatory levels. Although morphological and metabolic effects of combined hypoxia-salt stress are known in halophytes, the transcriptional mechanisms underlying these adjustments remain largely unexplored. In this study, we aimed to determine how the naturally adapted halophyte Salicornia europaea integrates hypoxia- and salt-specific responses at the transcriptional level to draw physiological conclusions about simultaneous stress interactions. To address this, we performed RNA sequencing of shoots and roots exposed to single and combined stress conditions. Our analysis revealed that 16% of genes were exclusively regulated under combined hypoxia-salt conditions, indicating distinct transcriptional reprogramming. Enhanced, divergent, and additive effects occurred across functional pathway categories, with divergent regulation predominating in both tissues. Pathway-level analysis uncovered unexpected strategies: up-regulation of sucrose biosynthesis genes, SUCROSE SYNTHASE (SUS), and TREHALOSE-6-PHOSPHATE PHOSPHATASE (TPP) suggested enhanced sucrose and trehalose metabolism, while down-regulation of invertases indicated strategic carbon flux redistribution. In addition, enhanced proline biosynthesis under combined stress indicated a shift towards improved osmoprotection. By combining transcriptomics with a physiological framework, we show how Salicornia employs non-additive and sometimes counterintuitive transcriptional strategies to coordinate carbon allocation, respiration, and osmotic balance. These findings highlight unique transcriptional adjustments that contribute to resilience under simultaneous stress.