## 4 Discussion  
In this study, gene-specific metagenomic PCR and qPCR amplification were used to analyze the environmental factors that influence the microbial community and nitrogen nutrition-related bacterium from three environmental sediment samples with distinct nitrogen source gradients. Phylogenetic analysis did not show distinct distribution differences in the communities among the nutrient-associated environments. Thus, we further analyzed the overall compositions and distribution of bacterial subdivisions. For example, in sample QL-H, the Proteobacteria were significantly affiliated with the Gammaproteobacteria (21.21%) and Betaproteobacteria (18.19%) clusters, whereas in the SR-W sample, they were more commonly associated with the Betaproteobacteria clusters, which were distributed on two distinct phylogenetic branches, and only one clone was clustered within the Alphaproteobacteria (Figure 1). In contrast, Proteobacteria was not the most abundant phylum in sample QL-V, and all the members were affiliated with the Betaproteobacteria class on distinct phylogenetic branches (Figure 1). The native composition of the microbial community in the QL-H sample was dominated by uncultured bacteria (39.30%) and the Cytophagales-Sphingobacteria group (18.18%). Interestingly, the community diversity in sample QL-V, which was collected in a neighboring village, displayed no relatively concentrated phyla, and uncultured bacteria dominated the clone library. Few clones from the sample QL-V sequences were affiliated with _Aquobacterium_, _Enterovibrio_, or Verrucomicroba. The sequences from the SR-W sample dataset were distinctly different from those of the other samples, and were assigned to _Aquobacterium_ (25%), Betaproteobacteria (25%), Bacteroidetes, and uncultured bacteria. Members of the beta class of the Proteobacteria were well represented under all the environmental conditions, whereas the abundances of the other classes differed significantly. The predominance of Proteobacteria in water samples of different quality suggests that the distribution of structurally simple prokaryotic consortia along microscale biogeochemical gradients is a unique and effective strategy by which bacteria meet their requirements for growth in otherwise inhospitable environments [26]. We also observed a clear difference in the community compositions in the SR-W and QL-H samples, which varied according to their levels of inorganic nitrogen. The genus _Aquobacterium_ was overrepresented in the high ammonia-nitrogen water because they have an efficient nitrate-dependent Fe(II) oxidation capacity, using nitrate as an electron acceptor [27]. Overall, the shifts in community composition along the gradients of dissolved organic carbon (DOC) and inorganic contaminants are similar to the patterns of growth efficiency and growth rates [28]. These results suggest that bacterial growth efficiency, abundance, and community composition are presumably constrained by the substrate concentrations of nitrogen compounds in most natural waters, with the possible exception of the most oligotrophic environments [29]. Functional biomarkers related to the physiology of specific bacteria, such as genes encoding unique enzymes involved in their specific biochemical metabolism [30], could offer a better alternative for exploring the diversity and population characteristics of bacterial communities. Furthermore, all the Hao proteins of the AOB clustered with _Nitrosomonas_, whereas no sequence clustered with the _Nitrosospira_ lineage (Figure 2). Similar studies have reported that _Nitrosomonas_ predominates in tannery wastewater treatment plants [10; 11; 12]. However, unlike the predominance of _N. europaea_ in various copiotrophic samples, such as laboratory-scale anaerobic ammonium-oxidizing reactors [31], full-scale modified Ludzack-Ettinger process wastewater treatment plants [11], and pilot-scale batch nitrifying reactors [32], none of our recovered clones clustered with _N. europaea_. Instead, _N. oligotropha_ and _N. ureae_ dominated our three samples.