Between 1999 and 2002, thecamoebian assemblages were analyzed in one hundred samples collected from tributaries of the Upper Vltava River (Šumava Mts., Czech Republic, Middle Europe). The Šumava Mountains comprise the largest forest complex in Central Europe that is still preserved in a near natural condition. Diverse fresh-water environments (springs, wetlands, peat bogs, creeks, rivers and ponds) characterize the area.

Thecamoebian tests were picked from dried 36–500 μm residues. In total, eighteen thecamoebian species were identified. The number of species per sample varies from one to thirteen, and the assemblages are characterized by dominance of Centropyxis orbicularis, C. aculeata, Pontigulasia compressa, Difflugia oblonga and Centropyxis arcula. A negative correlation (r = − 0.67) is notable between abundances of centropyxids and P. compressa. The negative correlation is caused by the different environmental conditions preferred by each taxon. Assemblages dominated by centropyxids originate mainly from standing water, whereas assemblages with common to abundant occurrences of P. compressa prefer running-water environments and substratum without coarse organic debris.

Following a flood event in August 2002, thecamoebian assemblages were more diverse and abundant. While reworking of thecamoebian tests from different biotopes during flooding probably caused the increase in diversity, a boom in the population of Centropyxis orbicularis after the flood event confirmed the opportunistic character of this species.

Boundary abundances of diagnostic species defined for flowing and standing waters in the forest area (= more than 20% of Pontigulasia compressa for flowing water and more than 50% of centropyxids for standing water) can be applied in interpretation of ancient environments. Similarly, changes in thecamoebian assemblages before and after the flood event can be used in paleoecology.

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