Five large deep subalpine lakes provide high prokaryotic diversity in the vertical gradient, during spring and summer stratification

We studied the prokaryotic assemblages in five subalpine lakes of different trophic conditions and mixing features, situated in Northern Italy and Southern Switzerland. L.Garda and L.Maggiore are both oligotrophic and oligomictic, L.Como is eutrophic and oligomictic, while L.Iseo and L.Lugano are eutrophic and meromictic. In early spring and summer the samples were taken at five depths (3 m, 10 m, 50 m, 200 m and maximum depth) and in situ hybridization (CARD-FISH) carried out using the following probes: Bacteria (EUB I-III), Thaumarchaeota (CREN537), Proteobacteria (ALF968,, BET42a, GAM42a), Cytophaga-Flavobacteria of Bacteroidetes (CF319a), Actinobacteria (HCG69a) and freshwater SAR11-cluster of Alphaproteobacteria termed LD12. In spring, at the maximum mixing, prokaryotes did not exhibit a vertical density gradient in the oligomictic lakes while the percentage of Betaproteobacteria increased with the depth in the meromictic lakes. Noteworthy was the dominance of Alphaproteobacteria in L.Como. In summer the prokaryotic community changed and niche differentiation occurred in almost all lakes: in L.Garda Actinobacteria dominate in the first 10 m and Bacteroidetes in the deeper layers. Actinobacteria dominate also in the first 10 m in L.Maggiore, L.Garda, L.Como, and were absent in L.Lugano and dominant in the whole water column in L.Iseo. Thaumarchaeota were confined to the hypolimnion during summer stratification, but present all over the water column in spring mixing. Uncultured bacteria of LD12-lineage were found in all lakes with higher percentage contributions in the epilimnion. However, in the eutrophic lakes Lugano and Iseo their relative contribution was less than in the oligotrophic lakes.