## 2 Materials and Methods
### Monitoring Design and Sampling  
We compared three sites (RS, VS and BS), each with a different community of benthic primary producers: epilithic diatoms and filamentous macroalgae on hard substrate (EA) at the RS site; submerged planerogams (SAV; _V. spiralis_ and _N. marina_) at the VS site; and microphytobenthos (MPB) at the BS site.  
The following sampling period was chosen in order to capture the seasonal growth phase of each primary producer assemblage: 12 April, 27 June, and 28 August 2017 at RS; 30 May, 31 July, and 3 October 2017 at VS and BS. Sampling dates are collectively reported in tables, figures and text as Early (late spring-early summer), Mid (midsummer) and Late (late summer-early fall) phases of the life cycle of the main components of the benthic primary producer community.  
At the RS site, six stones colonized by peripibpton were collected on each sampling date. After harvesting, the stones were immediately transferred into six distinct small Plexiglas microcosms (inner diameter 10 cm, height 20 cm) with water collected from the site. At the VS site, six sediment cores were sampled with Plexiglas tubes (inner diameter 10 cm, height 40 cm) on each date, while at the BS site, six cores (inner diameter 8 cm, height 30 cm) were also collected on the same dates. Simultaneously, at both VS and BS, five additional sediment cores (inner diameter 4 cm, height 20 cm) were sampled to establish the chemical and physical characteristics of the surface sediment. During sampling, extra care was taken to not disturb the superficial sediment. All samples between \(-\)1 and \(-\)4 m were manually collected by scuba diving. To ensure the maintenance and incubation of stones and cores in the laboratory, approximately 100 L of water were taken from each site.  
Once collected, both cores and microcosms were placed in thermal containers, submerged in water from the sampling site, and transported within 4 h to the laboratory at the University of Parma. Here, sediment cores and stones were housed in a thermostatic room, placed inside aerated incubation tanks (75 L) containing lake water from each site, and maintained at the same ambient temperature (\(\pm\)1 \({}^{\circ}\)C).  
\begin{table}
\begin{tabular}{c c} \hline \hline
**Watershed** & \\ \hline Area, lake included (km\({}^{2}\)) & 1842 \\ Mean altitude (m asl) & 1429 \\ \hline
**Lake** & \\ \hline Altitude (m asl) & 185 \\ Volume (km\({}^{3}\)) & 7.6 \\ Maximum depth (m) & 258 \\ Average depth (m) & 123 \\ Total Area (km\({}^{2}\)) & 60.9 \\ Litttoral Area (km\({}^{2}\)) & 5.0 \\ Theoretical renewal time (years) & 4.5 \\ \hline \hline \end{tabular}
\end{table}
Table 1: Main features of Lake Iseo and its watershed.  
Water temperature and conductivity were determined in situ with a multiparametric probe (YSI 556). Three water samples were also collected from each site at \(\sim\)50 cm above the sediment surface. Water samples were filtered (Whatman GF/F) and analyzed within 24 h to measure dissolved silica (DSi), ammonium (N-NH4\({}^{+}\)), nitrate and nitrite (N-NO\({}_{x}\)), and reactive phosphorus (SRP). Finally, total inorganic nitrogen (DIN) was calculated as DIN = N-NH4\({}^{+}\) + N-NO\({}_{x}\).