Morphological, Genetic, and Biochemical Traits Variation of Halodule uninervis at Different Microhabitats Along Egyptian Red Sea Coast

Halodule uninervis exhibits remarkable adaptability across environmental gradients in the Egyptian Red Sea. This study investigated five microhabitats ranging from the desiccation-prone, silty-sand flats of NIOF (location I: <0.5m depth, 41.35–41.54‰ salinity) to the thermally unstable sands of Wadi El Gemal (location V: ΔT = 34.74°C), integrating morphological, genetic, and biochemical analyses. At the morphological level, high-stress sites (I and V), exposed to intense light and heat, supported shorter shoots and roots (12–18% reduction), narrower leaves, and lower abundance traits that enhance stress tolerance. In contrast, more stable mid-depth NIOF (location II) and Marsa Alam (locations III and IV) showed longer shoots and roots with broader leaves and high abundance optimized for resource acquisition. Genomic fingerprints exposed striking patterns: shallow, high-stress populations (I/V) showed convergent evolution (0.87 genetic similarity) despite 120km separation, while adjacent moderate locations (II/III/IV) exhibited near-clonal profiles (0.94). The southern population (V) emerged as a genetic outlier (0.54 similarity with IV), likely shaped by strong specific microhabitat conditions. Metabolomic profiling further supported adaptive divergence: high-stress populations accumulated elevated levels of defensive phenolics (e.g., sinapinic acid, 2.1× higher) and structural hydrocarbons, while stable sites invested more in osmoprotective sugars (7.36% dry weight) and antioxidant compounds. This tripartite response morphological, genetic, and biochemical highlights the phenotypic plasticity and adaptive potential of H. uninervis. The results provide novel insights into how environmental gradients shape seagrass resilience, informing conservation strategies under climate change pressures.