## 1 Introduction  
The global biogeochemical nitrogen cycle has undergone dramatic changes in the past few decades. In particular, anthropogenic processes, including agricultural, industrial, and domestic activities, have resulted in an unprecedented increase in environmental nitrogen release. Overloading terrestrial ecosystems with ammonium, nitrate, and nitrite as the principal nitrogen pollutants has serious negative effects on human health, biodiversity, and water quality [1]. The coupled nitrification-denitrification and nitrification-anaerobic ammonium oxidation (anammox) processes mediated by environmental microorganisms are known to play important roles in the transformation and biogeochemical cycling of nitrogen, and probably contribute to the removal of up to 50% of the external dissolved inorganic nitrogen that enters the cosphere [2; 3]. Environmental conditions (i.e., carbon or nitrogen) can significantly influence the community structures and relative abundances of microorganisms [4]. The abilities of particular lineages of organisms to survive in specific environments may reflect relevant aspects of environmental nutrient availability [5; 6]. The diversity and structures of bacterial communities in lakes, estuaries [7], sea coasts [8; 9], and wastewater treatment plants [10; 11; 12] have been extensively investigated. Most studies of community bacterial phylogenies from single-source environmental samples have been based on the conventional analysis of 16S rRNA genes or Denaturing gradient gel electrophoresis (DGGE) analysis of specific genera [13]. However, the great divergence among different bacterial taxa is not directly related to the major environmental factors. Thus, it is important to investigate the variations and shifts in community composition regulated by the aquatic environmental factors [14; 15].  
To date, there has been few investigations available on the comparative analysis of microorganisms in lake environments where nutrients vary greatly within the same region, especially those involving nitrogen metabolisms [7]. The lake reservoir is influenced by the dynamic inflow tributaries adjoining residential areas, and may serve as a transitional zone from the eutrophication phylotypes of nitrifying and denitrifying bacteria to the oligotrophication ones. Therefore, a refined and targeted comparative description of the diversity of nitrifying and denitrifying communities in freshwater lakes with ammonia gradients is required in order to improve our understanding of the shifts in the nitrifying and denitrifying populations that occur with sharp differences in the environmental nitrogen status. This should also offer an opportunity to identify populations that are specific to those environments.  
The objectives of the present research were to investigate the pronounced community shifts in nitrifying and denitrifying populations in different environments (where there are sharp differences in the nitrogen and organic carbon status). A gene-specific metagenomic targeted PCR approach [16] was employed to comparatively characterize the nitrifying and denitrifying microbial communities from three environmental waters with different hydrological features, trophic statuses, and nitrogen pollution levels (Table 1). We expected that differences in the structures of nitrogen-transforming communities would accompany differences in nitrogen availability among three samples. We tested this by sequencing the hydroxylamine oxidoreductase (HAO) and nitrite reduction (copper-containing NirK and cytochrome cd1-containing NirS)-encoding genes of representative nitrifying and denitrifying bacteria within these samples, and compared their relative abundances with qPCR. These findings should extend our understanding of the bacterial communities that inhabit aquatic ecosystems and may have utility in the sustainable management of water resources.