Coastal blue carbon ecosystems sequester carbon, storing it as plant biomass and particulate organic matter in sediments. Recent studies emphasize the importance of incorporating dissolved inorganic and organic forms into carbon assessments. As sediment-stored organic matter decomposes, it releases dissolved inorganic carbon (DIC) and total alkalinity (TA), both of which are critical for regulating the partial pressure of CO2 (pCO2) and thus carbon sequestration. This study investigated the role of benthic DIC and TA fluxes in carbon sequestration within seagrass meadows in Dongsha Island’s inner lagoon (IL) during the winter and summer seasons. Chamber incubation experiments revealed elevated benthic DIC and TA fluxes compared to global averages (107 ± 75.9 to 119 ± 144 vs. 1.3 ± 1.06 mmol m−2 d−1 for DIC, and 69.7 ± 40.7 to 75.8 ± 81.5 vs. 0.52 ± 0.43 mmol m−2 d−1 for TA). Despite DIC fluxes being approximately 1.5 times higher than TA fluxes, water pCO2 levels remained low (149 ± 26 to 156 ± 18 µatm). Mass balance calculations further indicated that benthic DIC was predominantly reabsorbed into plant biomass through photosynthesis (−135 to −128 mmol m−2 d−1). Conversely, TA accumulated in the water and was largely exported (−60.3 to −53.7 mmol m−2 d−1), demonstrating natural ocean alkalinity enhancement (OAE). This study highlights the crucial role of IL seagrass meadows in coastal carbon sequestration through net autotrophy and carbonate dissolution. Future research should explore the global implications of these processes and assess the potential of natural OAE in other coastal blue carbon ecosystems.
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