Next to the benthic and pelagic compartments, the epiphyton of submerged macrophytes may offer an additional niche for ammonia-oxidizing bacteria in shallow freshwater lakes. In this study, we explored the potential activities and community compositions of ammonia-oxidizing bacteria of the epiphytic, benthic, and pelagic compartments of seven shallow freshwater lakes which differed in their trophic status, distribution of submerged macrophytes, and restoration history. PCR-denaturing gradient gel electrophoresis analyses demonstrated that the epiphytic compartment was inhabited by species belonging to cluster 3 of the Nitrosospira lineage and to the Nitrosomonas oligotropha lineage. Both the ammonia-oxidizing bacterial community compositions and the potential activities differed significantly between compartments. Interestingly, both the ammonia-oxidizing bacterial community composition and potential activity were influenced by the restoration status of the different lakes investigated.By converting ammonia into nitrite, ammonia-oxidizing bacteria (AOB) are responsible for the first step of the nitrification process (57, 58). Comparative 16S rRNA gene sequence analyses revealed assemblages of AOB in two monophyletic groups (17, 59). The main group, containing the genera Nitrosomonas, Nitrosospira, Nitrosovibrio, and Nitrosolobus, is affiliated with the beta subclass of Proteobacteria. The second group is affiliated with the gamma subclass and includes two species of the genus Nitrosococcus, retrieved and isolated exclusively from marine environments.AOB of the beta subclass have been detected in many different environments, from aquatic habitats (20,22,35,36,47,50,51,54,56) to soils (26)(27)(28)31) and building stones (48). The distribution patterns of distinct species of AOB depend on physiological differences between distinctive representatives (23) and on environmental parameters like ammonia concentration (5, 49, 51), pH and temperature (21, 42), oxygen availability (6, 16, 43), and salinity (10, 49). Horz et al. (19) demonstrated that AOB from a grassland soil are also able to respond to multifactorial global changes. AOB are therefore considered a model group in microbial ecology studies (27). However, it remains difficult to couple results obtained from physiological experiments conducted in the laboratory with isolated strains to nitrification activities observed in the environment from which the strains were isolated (27).AOB are known to grow either free-living or attached. For example, compared with the water column of aquatic environments, solid-phase habitats, such as sediment, particulate material, and aquatic macrophytes, seemed to be differently (35,40,50) and more densely populated with nitrifying bacteria (12,33,34). This surface-attached growth has been proposed to offer resilience against environmental constraints (41). Moreover, the formation of a biofilm on surfaces provides significant benefits for AOB of the Nitrosomonas lineages that are able to produce extracellular polymeric materials...