Diversity and distribution of amoA-type nitrifying and nirS-type denitrifying microbial communities in the Yangtze River estuary
Coupled nitrification–denitrification plays a critical role in the removal of excess nitrogen, which is chiefly caused by humans, to mitigate estuary and coastal eutrophication. Despite its obvious importance, limited information about the relationships between nitrifying and denitrifying microbial communities in estuaries, and their controlling factors have been documented. We investigated the nitrifying and denitrifying microbial communities in the estuary of turbid subtropical Yangtze River (YRE), the largest river in Asia, by analyzing the ammonia monooxygenase gene amoA, including archaeal and bacterial amoA, and the dissimilatory nitrite reductase gene nirS using clone libraries and quantitative PCR (qPCR). The diversity indices and rarefaction analysis revealed a quite low diversity for both β-proteobacterial and archaeal amoA genes, but qPCR data showed significantly higher amoA gene copy numbers for archaea than β-proteobacteria. Compared with the amoA gene, a significantly higher level of diversity but lower gene copy numbers were found for the nirS gene. Nitrification and denitrification rates based on 15N incubation experiments supported gene abundance data as denitrification rates were below detection limit, suggesting lower denitrification than nitrification potential. In general, the abundances of the amoA and nirS genes were significantly higher in the bottom samples than the surface ones, and in the high-turbidity river mouth, were significantly higher in the particle-associated (> 3 μm) than the free-living (0.2 ~ 3 μm) communities. Notably, positive correlations between the amoA and nirS gene abundances suggested potential gene-based coupling between nitrification and denitrification, especially for the particle-associated assemblages. Statistical analysis of correlations between the community structure, gene abundances and environmental variables further revealed that dissolved oxygen and total suspended material might be the key factors controlling community spatial structure and regulating nitrification and denitrification potentials in the YRE ecosystem.