Community structure, abundance, and in situ activity of nitrifying bacteria in river sediments as determined by the combined use of molecular techniques and microelectrodes

The community structure, spatial distributions, and in situ activity of ammonia-oxidizing bacteria (AOB) representing the Betaproteobacteria and nitrite-oxidizing bacteria (NOB) representing the genus Nitrospira in three different river sediments with different pollution sources and levels along the Niida River, Hachinohe, Japan, were investigated by the combined use of 16S rRNA gene-cloning analysis, real-time quantitative polymerase chain reaction (RTQ-PCR) assays, and microelectrodes. The goal of this research was to evaluate the contribution of nitrifying activity in the sediment to the overall nitrogen elimination rate in this river. The 16S rRNA gene-cloning analysis revealed that the community structures of AOB and Nitrospira-like NOB are present in three sediments. On the basis of the results of 16S rRNA gene-cloning analysis, the RTQ-PCR assay using a TaqMan probe was developed and optimized for the quantification of the Nitrospira-like NOB. In the sediments, AOB specific 16S rRNA genes were detected in the range of 10(6) to 10(7) copies/cm(3) and evenly distributed over the sampled sediment depth (0-5 mm), whereas the Nitrospira-like NOB 16S rRNA gene copy numbers per cm(3) were 1-2 orders of magnitude higher than the AOB copy numbers. Under light conditions, intensive oxygenic photosynthesis occurred in the surface and increased the maximal O-2 concentration and O-2 penetration depth in all sediments. This concomitantly stimulated nitrifying bacteria present in diurnally anoxic deeper zones and expanded nitrification zones, which consequently increased the total NH4+ consumption rate in the sediment (i.e., total NH4+ flux into the sediment). The results suggested that the in situ nitrifying activity was restricted mainly to the surface 2 mm of the sediment and linked with photosynthetic activity, which obviously plays an important role in nitrogen elimination in this river.