## 5 Conclusions  
One of the main findings of our study is that macro- and microalgae communities on rocky substrates behave as a DSi sink and are a source of inorganic nitrogen and phosphorus for the water column. In contrast, littoral sediments colonized by submerged aquatic vegetation and microphotenthos behave as a DSi source for the water column and as a sink for inorganic nitrogen and phosphorus. _Vallisneria spiralis_, in particular, can transfer DSi from pore-water to the overlying water column through BSi synthesis and mineralization. This pathway can be a relevant DSi source, compensating for possible Si losses due to sedimentation and segregation in the deeper water mass. This is a key issue for oligomatic and, especially, meromictic lakes, which do not completely overturn. Two questions, however, remain unanswered: first, to what extent does the missing DSi influence lake productivity, especially in relation to the siliceous components of the phytoplankton community; and, second, how will the DSi budget downstream in the outflowing river be decreased as a result of this DSi shortage.  
The capacity of SAV to simultaneously control both Si and N and P cycling depends on the health status of the community. This aspect should not be ignored when considering the anthropogenic impact from watersheds and lake surroundings. Recent studies have demonstrated that SAV meadows can suffer deterioration and leaf detachment at a greater rate than the expected physiological one, with even uprooting events taking place. A challenging issue is to assess what the fate of such organic matter bulk is, and how this can contribute to self-sustain lake deterioration.  
The following are available online at [[http://www.mdpi.com/2073-4441/11/10/2140/s1](http://www.mdpi.com/2073-4441/11/10/2140/s1)]([http://www.mdpi.com/2073-4441/11/10/2140/s1](http://www.mdpi.com/2073-4441/11/10/2140/s1)). Table S1. Features of organic matter (OM), biogenic silica (BSi), organic nitrogen (N), organic phosphorous (P), chlorophyll a (Chl-a) and phaeopignments (Pha) in the 0-2 cm sediment horizon at the three investigated sites (RS = rocky shores; VS = vegetated sediments; BS = bare sediments). All data represents the mean \(\pm\) standard error (standard error in parenthesis), n.a. = not available. Table S2. Features of organic matter (OM), biogenic silica (BSi), organic nitrogen (N), organic phosphorous (P), chlorophyll a (Chl-a) and phaeopignments (Pha) in the 2-5 cm sediment horizon at the three investigated sites (RS = rocky shores; VS = vegetated sediments; BS = bare sediments). All data represents the mean \(\pm\) standard error (standard error in parenthesis), n.a. = not available.  
**Author Contributions:** [PERSON], [PERSON] and [PERSON], conceived the experimental design, processed data, and wrote the manuscript. [PERSON] coordinated the experimental activity. [PERSON], [PERSON], [PERSON], [PERSON], [PERSON] contributed field and laboratory work. [PERSON] provided classification of benthic phanerogams and macroalgae.  
**Funding:** This research is part of the ISEO (Improving the lake Status from Eutrophy to Oligotrophy) project and was made possible by CARIPLO foundation grant number 2015-0241. A.S. was partially supported by the EOMORES project (H2020, project number 730066), D.N. was partially supported by Lombardy Region within the project \"Assessment of the limnological status of the Lombardy Region lakes and of nutrients loads formation in heavily exploited watersheds\".  
**Conflicts of Interest:** The authors declare no conflict of interest.