Spatial and temporal variability of carbon budgets of shallow South African subtropical estuaries

Highlights: • Subtropical estuarine communities are net heterotrophic during the year. • Emissions vary significantly between seasons and sites. • Estuarine mouth status (permanently open or prolonged closure) influences magnitude of carbon fluxes. • First comprehensive direct estimation of carbon and nutrient fluxes in South African estuaries Estuarine carbon fluxes constitute a significant component of coastal CO₂ emissions and nutrients recycling, but high uncertainty is still present due to the heterogeneity of these areas. Although South Africa has nearly 300 estuaries, very little is known about their contribution to carbon emissions or sequestration. This study aims to provide a first estimation of the carbon emissions and nutrient fluxes of South African sub-tropical estuaries through a direct quantification of respiration, primary production and nutrient regeneration of benthic and planktonic communities. In order to account for the extreme variability in subtropical estuarine areas, due to seasonality in rainfall, two estuaries with opposite characteristics were studied; the temporarily open/closed Mdloti Estuary subjected to strong anthropic pressure, and the permanently open Mlalazi Estuary located in a natural reserve. Field deployment of benthic chambers and clear/dark bottles assessed oxygen, ammonia and phosphate fluxes of both benthic and planktonic communities. An inverse pattern between benthic and pelagic primary production was found in both estuaries. Different drivers related to mouth status and sediment characteristics were identified in the two estuaries. The annual average carbon emission indicates that the two systems are heterotrophic over the year releasing substantial CO₂ emissions into the atmosphere. Results show that carbon fluxes in subtropical estuaries are extremely variable in space and time. Future up-scaling carbon estimations need to account for those small scale and regional dynamics.