## 2 Materials and Methods
### Core Incubation Experiment  
All cores were pre-incubated with 50 mL of filtered brackish estuarine water for about 1 h to ensure water saturation of the pore space. Two and four core replicates, respectively, were used for the measurement of dissolved oxygen (DO) and nutrient fluxes. Two empty core liners served as control incubations. For DO measurements cores were adjusted to a headspace of about 500 mL in the liners, completely filled with filtered (GF/F, 0.45 \(\upmu\)m) estuarine water and sealed without disturbance of the sediment surface. The sealing caps had holes to accommodate a LDO dissolved oxygen sensor (Hach-Lange, Berlin, Germany). Measurements of DO concentration and saturation, and water temperature were done half hourly. For nutrient measurement 500 mL of filtered estuarine water were added and cores were covered to prevent evaporation. Water samples were drawn hourly through a sampling port in the cover cap. Using this port, the extracted volume was replaced with demineralized water to maintain the incubated volume. To prevent stratification of the water column, incubated water in all cores was permanently circulated using a peristaltic pump. A pump rate of 2 to 2.5 L\(\cdot\)h\({}^{-1}\) was chosen to ensure complete circulation of the volume between samplings, while preserving an undisturbed sediment surface. The incubation lasted for eight hours under constant light and temperature conditions. Ambient temperature was chosen according to average seasonal air temperature to be 16 \({}^{\circ}\)C in March and 25 \({}^{\circ}\)C in October (Table 1). Throughout the incubation, the water temperature remained nearly constant, with maximum standard deviations of 0.7 \({}^{\circ}\)C in March and 0.4 \({}^{\circ}\)C in October. Following incubation in the light the overlying water was replaced, and the cores were reused for dark incubation.  
\begin{table}
\begin{tabular}{c c c c c c c c c c} \hline \hline  & \multicolumn{6}{c}{**Initial Concentrations [\(\upmu\)M]**} & \multicolumn{3}{c}{**Temperature [\({}^{\circ}\)C]**} \\ \hline
**Date** & **NO\({}_{3}\)**-** & **NO\({}_{2}\)**- & **NH\({}_{4}\)**+ & **PO\({}_{4}\)**-** & **Si** & **DOC** & **O\({}_{2}\)** & **Monthly** & **During** \\  & & & & & & & & & **Average** & **Incubation** \\ \hline
16 March 2011 & 197.0 & 5.4 & 9.0 & 2.8 & 76.5 & 383.0 & 308.5 & 15.3 & 16.0 \\
3 October 2011 & 84.9 & 4.3 & 19.1 & 1.5 & 94.2 & 371.5 & 223.1 & 25.6 & 25.0 \\ \hline \hline \end{tabular}
\end{table}
Table 1: Initial concentrations of dissolved nutrients and oxygen at the beginning of the incubation experiment, as well as monthly average ambient air temperature and air temperature during incubation.  
Fluxes of dissolved oxygen and nutrients in individual incubation cores were calculated by linear regression of concentration (corrected for dilution) over time (nine times: initial concentrations plus eight hourly samples). Outliers were removed from the regression according to the method by [PERSON] _et al._[52]; out of a total of 1323 data pairs, 22 were removed. In no case did the removal change the significance of correlations. Hourly fluxes are equal to the slope of the outlier-free regression line if linear correlation was significant (\(p\leq 0.05\)); otherwise net fluxes are defined as zero. Total sediment nutrient fluxes were calculated as the difference of averages in sediment incubations and controls. Statistical comparison of sediment treatment and control fluxes revealed low power (alpha) of \(t\)-tests due to small sample size. Where alpha was high enough to yield reliable results, treatment and control fluxes were significantly different at \(p<0.05\). Negative values represent influxes, positive ones represent effluxes. Dissolved inorganic nitrogen (DIN) fluxes were calculated as sum of nitrate (NO3-), nitrite (NO2-) and ammonium (NH4+) sediment fluxes.