Recalcitrant organic carbon in deep soils plays a greater role in soil carbon sequestration under tidal flat than vegetated salt marsh

Sea-level rise significantly impacts soil organic carbon (SOC) pool in estuarine wetlands by altering hydrological, biological, and biogeochemical processes. However, the mechanisms regulating SOC accumulation and stability remain incompletely understood. In this study, we employed a space-for-time substitution by selecting four distinct regions within the intertidal zone comprising vegetated and non-vegetated habitats. Our results showed that soil salinity primarily drove vegetation composition. SOC content in 0–20 cm layer decreased from land to sea (increasing salinity), while SOC content below 40 cm in the tidal flat exceeded that in vegetated habitats. SOC was dominated by recalcitrant organic carbon (ROC) in the tidal flat, with lower carbon activity, carbon activity index, and geometric mean of active organic carbon, suggesting higher stability. Vegetated habitats had greater carbon pool index and carbon pool management index in 0–40 cm, but tidal flat showed higher values below 40 cm. Multivariate analyses revealed total nitrogen as the top driver of SOC accumulation, with soil water content critical below 60 cm. Salinity indirectly modulated SOC burial via vegetation composition/productivity. We conclude that vegetation governs surface SOC accumulation in vegetated habitats, whereas tidal flats exhibit greater blue carbon storage potential, driven by “water-salinity-mineral” stabilization. Therefore, protecting tidal flats is crucial for blue carbon sequestration, and future management strategies should implement soil layer-specific and vegetation zone-specific approaches to minimize anthropogenic disturbances.