## 2 Materials and Methods
### Benthic Fluxes and Benthic Metabolism  
In the laboratory, cores and microcosms were immediately left to stabilize \(\approx\)12 h in lake water with the upper end open and completely submerged. During maintenance and incubation, the water inside the cores and microcosms was gently stirred, avoiding sediment resuspension, using magnetic stirrs suspended within each core, and driven with a magnet rotated at 40 rpm by an external motor. The day after sampling, the cores were first incubated in darkness and, subsequently, in light to measure water sediment fluxes. To begin the incubation, the water level in the tank was lowered below the core edges and a water sample was taken from each core to determine the initial chemical characteristics. In order to start the incubation process, the upper opening of the cores was closed with a floating Plexiglas lid. At the end of the incubation, the cores were opened and the water was sampled from each core to determine final chemical characteristics. Fluxes of oxygen and nutrients were paired for dark and light incubation -i.e., measured on the same cores. Following the dark incubation, the incubation tanks were re-filled with water from the site, the cores re-submerged and left uncapped for one hour to re-equilibrate prior to start light incubations. Light conditions were obtained with adjustable halogen lamps; light intensity (400-600 \(\mu\)E m\({}^{-2}\) s\({}^{-1}\)) was set on the basis of the average daily radiation of the sampling day recorded with a PAR quanto-photo-radiometer (Delta OHM, model HD 9021, Padova, Italy). Incubation time for both dark and light conditions ranged between 2 and 5 h. Based on previous incubations, the time was set in relation to water temperature and the dominant primary producer community inside the cores in order to obtain an oxygen variation of \(<\)20% of the initial concentration.  
Water samples were collected with plastic syringes. Subsamples were transferred into glass tubes (Labco Exetainer(r), Lampeter, Wales, UK) to which Winkler reagents were added to determine dissolved O\({}_{2}\). The remaining water was filtered through Whatman GF/F glass fiber filters: to determine DSi, N-NO\({}_{x}\) and N-NH\({}_{4}\)\({}^{+}\) samples were stored in polyethylene vials, while to measure SRP, glass tubes were used. Analyses for O\({}_{2}\) determination were performed immediately after collection; samples for determination of SRP and N-NO\({}_{x}\) were stored at 4 \({}^{\circ}\)C and analyzed within 24 h, while samples for DSi and N-NH\({}_{4}\)\({}^{+}\) were frozen and subsequently analyzed. Fluxes of O\({}_{2}\) and nutrients were quantified as the change over time of the concentration of each parameter using the Formula (1) ([35]):  
\[F_{x}=\frac{\left(C_{f}-C_{0}\right)\times V}{A\times\Delta t} \tag{1}\]  
where, \(F_{x}\) is the flux of the x chemical species (mg m\({}^{-2}\) h\({}^{-1}\)), \(C_{f}\) is the final concentration of x (mg L\({}^{-1}\)), \(C_{0}\) is the initial concentration of x (mg L\({}^{-1}\)), \(V\) is the volume of the water column (L), \(\Delta t\) is the incubation time (h) and \(A\) is the sediment surface area inside the core (m\({}^{2}\)).  
As a result of the irregular shape of the stones, the surface area of each rock was carefully measured using the foil-wrapping technique [36]. In short, the surface of each rock was wrapped with close-fitting aluminum foil, trimming any excess, and then weighing the foil wrap. A regression equation based on the weight and area relationship of aluminum foil (\(n=10\)) was used to convert rock foil wrapping weights to areas.  
Net daily sediment-water fluxes were calculated as the sum of the light and dark rates multiplied by the average light and dark phase duration.