Insights into the Variations of Hao-Dependent Nitrifying and Nir-Dependent Denitrifying Microbial Communities in Ammonium-Graduated Lake Environments

Biological nitrification and denitrification play significant roles in nitrogen-associated biogeochemical cycles. However, our understanding of the spatial scales at which microbial communities act and vary is limited. We used gene-specific metagenomic PCR to explore changes in nitrifying and denitrifying microbial communities within pristine lake and its branches, where the ammonium and dissolved organic carbon (DOC) concentrations form a gradient. The biomarkers hydroxylamine oxidoreductase and nitrite reductase genes indicated that strong relationships exist between the diversities and community structures of denitrifiers and ammonium gradients. It showed that the Nitrosomonas oligotropha cluster dominates the nitrifying bacteria in low-nutrition environments, while a new Nitrosomonas ureae cluster accounted for nearly 80% of the nitrifying bacteria in high-nitrogen environments. The distribution and diversity of nirS/K-dependent denitrifiers in the various habitats were similar, but predominantly affiliated with unknown clusters. Moreover, the abundance of all the hao genes dramatically outnumbered that of nir genes. The relative abundance of hao was clearly higher during eutrophication (13.60%) than during oligotrophy (5.23%), whereas that of nirS showed opposite tendencies. Overall, this study provides valuable comparative insights into the shifts in nitrifying and denitrifying microbial populations in lake environments with ammonium gradients, suggesting that unique dominant denitrifiers probably play an important role in the nitrogen cycle.