Peatbogs have both horizontal and vertical differences in moisture, pH, light and nutrient availability. Micro-distribution of testate amoebae taxa has been observed along the Sphagnum stem but there is no data concerning the vertical micro-distribution of protozoa in water column under the peatbog surface and in the interstitial waters. The research was made in a small (ca 16 ha) peatbog complex in the eastern Poland. Vertical microzonationof testate amoebae and ciliates in relation to physical, chemical and biological parameters (peat porosity, temperature, dissolved oxygen, chlorophyll a, TN, TP, DOC and TOC) in Sphagnum hollows, mud bottom hollows and interstitial waters in peatbog were studied. Samples were taken once a month from April to November 2009 from three layers: free water mass up to 10 cm (FW), bottom water (BW) and interstitial, pore water – IW (water between particles of peat on depth 20–25 cm). During each sampling occasion 3 samples were collected from each site. At each type of micro-habitat and each sampling date water was sampled using a plexiglass core. The water column sampled from the top surface to the bottom was 25 cm high. Interstitial waters were collected from mini-piezometers located into the peat. Temperature, dissolved oxygen, conductivity, chlorophyll a and nutrients contents were always lower in interstitial water than in free and bottom waters. The highest numbers of testate amoebae and ciliates taxa occurred in the bottom water (31 and 13 taxa, respectively) and became much lower in interstitial water (17 and 5 taxa, respectively). The density and biomass of protozoa differed significantly between the studied layers, with the lowest numbers in the interstitial water and the highest in the bottom water. Ordination analysis indicated that chlorophyll a, TOC and TP can strongly regulate the abundance and species composition of protozoa. The RDA ordination showed that the testate amoebae species can be divided into three groups associated with: 1) free water mass, 2) bottom water and 3) interstitial water, while the ciliate species into two groups associated with: 1) interstitial water and 2) free water mass and bottom waters. The free water mass and bottom water were dominated by mixotrophic taxa, whereas the deepest layer showed the increase of the contribution of small, bacterivorous species. In all the examined micro-habitats the highest abundance and biomass of these microorganisms occurred in early spring and late autumn, while the lowest values were recorded in late summer.
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