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The study of the hydrodynamics of the hypolimnion of a deep holo-oligomictic lake (Lake Maggiore, Northern Italy, zmax¼370 m) during the last 28 years showed that hypolimnetic waters remained isolated, not exchanging with the mixing zone even in winter when the full overturn conditions are most likely. The thickness of the isolated layer can range from 100 to 300 m. Thus, water masses of variable size reside in the lake for many years, and their physical and chemical conditions remain relatively unaffected by seasonal variability and epilimnetic imputs. In the hypolimnetic waters prokaryote abundance is three times lower than in the mixing layer but cell size is significantly higher. In addition, the relative abundance of Archaea and Crenarchaeota increases with depth in respect to that of Bacteria. The heterogeneous distribution of the two domains within the habitat can be attributed to the existence in the same environment of isolated water masses.
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