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Net ecosystem production (NEP) by submerged aquatic vegetation plays a substantial role in capturing atmospheric carbon dioxide into aquatic ecosystems. In lakes and estuaries, the net uptake of carbon dioxide by submerged aquatic vegetation is mediated by stratification of the water column which suppresses the vertical flux of carbon dioxide between the upper and lower layers. The presence of submerged aquatic vegetation can also affect the strength of stratification such that the interactions between vegetation, stratification, and NEP can moderate the carbon dioxide emissions. Since stratification can occur in lakes and estuaries, there is need for a new numerical approach able to consider the effect of submerged aquatic vegetation on stratification, NEP, and carbon dioxide. This study aims to develop a model to investigate how stratification, mediated by vegetation density and flexibility, affects the partial pressure of carbon dioxide (pCO2) and dissolved inorganic carbon (DIC). After initial parameterization of coefficients based on experimental work, horizontal and vertical variations in DIC were successfully modeled by a spatially (horizontally) integrated DIC (SiDIC) model, which was validated with field observations from an estuarine and freshwater lake case study. The SiDIC model was able to reproduce the pCO2 changes between daytime and nighttime throughout the water column. Sensitivity tests showed that the fluctuation of pCO2 was controlled by the suppression of stratification due to the density of submerged aquatic vegetation. The results highlight the importance of resolving vegetation-induced stratification when modeling the carbon budget within freshwater lakes and coastal environments.
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