Ammonia-oxidizing Archaea (AOA) play an important role in the oxidation of ammonia in terrestrial, marine, and geothermal habitats, as confirmed by a number of studies specifically focused on those environments. Much less is known about the ecological role of AOA in freshwaters. In order to reach a high resolution at the Thaumarchaea community level, the probe MGI-535 was specifically designed for this study and applied to fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) analysis. We then applied it to a fine analysis of diversity and relative abundance of AOA in the deepest layers of the oligotrophic Lake Maggiore, confirming previous published results of AOA presence, but showing differences in abundance and distribution within the water column without significant seasonal trends with respect to Bacteria. Furthermore, phylogenetic analysis of AOA clone libraries from deep lake water and from a lake tributary, River Maggia, suggested the riverine origin of AOA of the deep hypolimnion of the lake.

Limnological Station Institute of Plant Biology University of Zurich Seestrasse 187 8802 Kilchberg Switzerland

Limnological Station Institute of Plant Biology University of Zurich Seestrasse 187 8802 Kilchberg Switzerland ; Institute of Hydrobiology Biology Centre CAS Na Sádkách 7 370 05 České Budějovice Czech Republic

Microbial Ecology Group CNR Institute of Ecosystem Study Largo Tonolli 50 28922 Verbania Italy

Microbial Ecology Group CNR Institute of Ecosystem Study Largo Tonolli 50 28922 Verbania Italy ; Limnological Station Institute of Plant Biology University of Zurich Seestrasse 187 8802 Kilchberg Switzerland

Microbial Ecology Group CNR Institute of Ecosystem Study Largo Tonolli 50 28922 Verbania Italy ; Microb and Co Association for Microbial Ecology Viale XX Settembre 45 95128 Catania Italy

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