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To elucidate bacterial population dynamics in an aquifer, we attempted to reveal the impact of protozoan grazing on bacterial productivity and community structure by an in situ incubation experiment using a diffusion chamber. The abundance and vertical distribution of bacteria and protozoa in the aquifer were revealed using wells that were drilled in a sedimentary rock system in Itako, Ibaraki, Japan. The water column in the wells possessed aerobic and anaerobic layers. Active bacterial populations under the grazing pressure of protozoa were revealed through in situ incubation with grazer eliminating experiment by the filtration. On August 19, 2003, the total number of bacteria (TDC) decreased from 1.5 × 106 cells ml- 1 at 2.2 m depth to 3.0 × 105 cells ml- 1 at 10 m depth. The relative contribution of the domain Bacteria to TDC ranged between 63% and 84%. Protozoa existed at a density of 4.2 × 104 to 1.9 × 105 cells ml- 1 in both aerobic and microaerobic conditions. A grazing elimination experiment in situ for 6 days brought about clearly different bacterial community profiles between the 2.2 m and 10 m samples. The bacterial composition of the initial community was predominantly β- and γ -proteobacteria at 2.2 m, while at 10 m β-, α - and γ -proteobacteria represented 56%, 26% and 13% of the community, respectively. The distribution of bacterial abundance, community composition and growth rates in the subsurface were influenced by grazing as well as by geochemical factors (dissolved oxygen and concentrations of organic carbon, methane and sulfate). Results of the in situ incubation experiment suggested that protozoan grazing contributes significantly to bacterial population dynamics. [ABSTRACT FROM AUTHOR]