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The introduction of embankment seawalls to limit the expansion of the exotic C4 perennial grass Spartina alteniflora Loisel in eastern China’s coastal wetlands has more than doubled in the past decades. Previous research focused on the impact of sea embankment reclamation on the soil organic carbon (C) and nitrogen (N) stocks in salt marshes, whereas no study attempted to assess the impact of sea embankment reclamation on greenhouse gas (GHG) fluxes in such marshes. Here we examined the impact of sea embankment reclamation on GHG stocks and fluxes of an invasive Spartina alterniflora and native Phragmites australis dominated salt marsh in the Dongtai wetlands of China’s Jiangsu province. Sea embankment reclamation significantly decreased soil total organic C by 54.0% and total organic N by 73.2%, decreasing plant biomass, soil moisture, and soil salinity in both plants’ marsh. It increased CO2 emissions by 38.2% and 13.5%, and reduced CH4 emissions by 34.5% and 37.1%, respectively, in the Spartina alterniflora and Phragmites australis marshes. The coastal embankment wall also significantly increased N2O emission by 48.9% in the Phragmites australis salt marsh and reduced emissions by 17.2% in the Spartina alterniflora marsh. The fluxes of methane CH4 and carbon dioxide CO2 were similar in both restored and unrestored sections, whereas the fluxes of nitrous oxide N2O were substantially different owing to increased nitrate as a result of N-loading. Our findings show that sea embankment reclamation significantly alters coastal marsh potential to sequester C and N, particularly in native Phragmites australis salt marshes. As a result, sea embankment reclamation essentially weakens native and invasive saltmarshes’ C and N sinks, potentially depleting C and N sinks in coastal China’s wetlands. Stakeholders and policymakers can utilize this scientific evidence to strike a balance between seawall reclamation and invasive plant expansion in coastal wetlands.

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