Distribution and activity of nitrifying bacteria in natural stream sediment versus laboratory sediment microcosms

Nitrification was studied with microsensors and fluorescence in situ hybridization (FISH) in sandy sediment of a small lowland stream. Comparative measurements were performed in both intact field sediment (‘natural sediment’) and sediment from the same site after processing for a laboratory incubation experiment (‘manipulated sediment’). In natural sediment, the nitrification activity and abundance of nitrifiers were markedly low. In contrast, nitrification activity in manipulated sediment (sieved, homogenized, and incubated for 5 wk in the laboratory with NH4-enriched stream water) was significantly higher. Similarly, abundances of NH4-oxidizing β-proteobacteria (AOB) and NO2-oxidizing Nitrospira spp. directly at the sediment surface were markedly higher than in natural sediment. AOB mixed into deep sediment layers by homogenization disappeared more quickly than Nitrospira spp., suggesting that the latter were more persistent under anoxic conditions. Higher activity and abundance of nitrifiers near the sediment–water interface of manipulated sediment were explained by (1) the additional NH4 supply via the overlying water and (2) the adverse conditions for nitrification in the field. In conclusion, the snapshot measurement in natural sediment revealed the spatial heterogeneity created by stream dynamics, whereas the sediment manipulation provided semi-natural microcosms with reduced heterogeneity suitable for factorial experiments.