Diversity and distribution of <i>amoA</i>-type nitrifying and <i>nirS</i>-type denitrifying microbial communities in the Yangtze River estuary

Coupled nitrification–denitrification plays a critical role in the removalof excess nitrogen, which is chiefly caused by humans, to mitigate estuaryand coastal eutrophication. Despite its obvious importance, limitedinformation about the relationships between nitrifying and denitrifyingmicrobial communities in estuaries, and their controlling factors have beendocumented. We investigated the nitrifying and denitrifying microbialcommunities in the estuary of turbid subtropical Yangtze River (YRE), thelargest river in Asia, by analyzing the ammonia monooxygenase geneamoA, including archaeal and bacterial amoA, and thedissimilatory nitrite reductase gene nirS using clone libraries andquantitative PCR (qPCR). The diversity indices and rarefaction analysisrevealed a quite low diversity for both β-proteobacterial and archaealamoA genes, but qPCR data showed significantly higher amoAgene copy numbers for archaea than β-proteobacteria. Compared with theamoA gene, a significantly higher level of diversity but lower genecopy numbers were found for the nirS gene. Nitrification anddenitrification rates based on ¹⁵N incubation experiments supported geneabundance data as denitrification rates were below detection limit,suggesting lower denitrification than nitrification potential. In general,the abundances of the amoA and nirS genes weresignificantly higher in the bottom samples than the surface ones, and in thehigh-turbidity river mouth, were significantly higher in theparticle-associated (> 3 μm) than the free-living(0.2 ~ 3 μm) communities. Notably, positive correlationsbetween the amoA and nirS gene abundances suggestedpotential gene-based coupling between nitrification and denitrification,especially for the particle-associated assemblages. Statistical analysis ofcorrelations between the community structure, gene abundances andenvironmental variables further revealed that dissolved oxygen and totalsuspended material might be the key factors controlling community spatialstructure and regulating nitrification and denitrification potentials in theYRE ecosystem