Hydrological inundation threshold regulates the carbon source-sink transition in unvegetated tidal flats

Unvegetated tidal flats cover extensive areas of global coastlines, but their role in atmospheric CO₂ exchange remains poorly understood. Here we investigate how hydrological regimes regulate carbon uptake in these ecosystems through a marsh organ experiment in the subtropical Zhangjiang Estuary, China that integrated sediment-atmosphere CO₂ and CH₄ flux measurements, porewater geochemistry, and metagenomic sequencing. We identified a site-specific hydrological transition in which sediment-atmosphere CO₂ exchange shifted from a weak source to sustained net uptake under more frequent inundation, with the transition occurring around an annual inundation frequency of approximately 10-30% in this experimental system. This transition coincided with declining porewater NO₃^-/Cl^- and SO₄^2-/Cl^- ratios and increasing pH, dissolved CO₂ concentration, and carbonate system derived estimated alkalinity, consistent with enhanced anaerobic redox processes and alkalinity-associated CO₂ dissolution and retention. Although CH₄ emissions increased under frequent inundation, incorporating CH₄ into global warming potential did not substantially offset the CO₂ sink transition. Metagenomic analyses further showed an enrichment of rTCA-related carbon-fixation taxa under frequent inundation, indicating greater microbial autotrophic carbon-fixation potential. This functional potential was associated with porewater geochemical changes and increased microbial biomass carbon, supporting the possibility of hydrologically modulated geochemical-microbial coupling during the CO₂ source-sink transition. Together, our results unveil a previously unrecognized mechanism in which a hydrologically-modulated geochemical-microbial coupling drives CO₂ uptake in frequently inundated sediments. These findings extend current blue carbon frameworks by highlighting the previously overlooked role of unvegetated tidal flats in coastal carbon cycling and climate regulation.