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 SO42-/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.