Global urbanization has resulted in local habitat fragmentation, influencing ecological processes and
biodiversity conservation. However, little is known about the diversity and distribution of microbial
communities across urban biotopes. Here, we compared testate amoeba communities in Moscow (63
samples) and Xiamen (69 samples) urban parks across four biotopes (tree hole, moss, soil, and sediment)
to better understand microbial diversity and ecological processes shaping microbial communities. A total
of 116 morphospecies (31 genera), corresponding to 90 in Moscow and 84 in Xiamen, were identified
using light microscopy. The species richness per sample (mean ± standard error) was higher in Moscow
parks (14 ± 1 species, n = 63) than Xiamen parks. The mean species richness per biotope was highest in
the mosses (13 ± 1 species, n = 33). 13–26% of the total species richness was shared by all biotopes,
indicating the ubiquitous distribution of testate amoeba morphospecies. The community composition in
different biotopes markedly differed in both Moscow and Xiamen regions. Community connectivity
varied among biotopes, and community complexity and dynamics were substantially stronger in soil and
sediment. The stochastic processes explained a significantly high percentage of community composition
in all biotopes (57–81%). The standardized effect size for C-score in all biotopes changed from 1.48 to
6.92, indicating the enhanced significance of deterministic processes for the testate amoeba
communities. The different relative importance of stochastic or deterministic processes in four studied
biotopes suggests that factors influencing the testate amoeba communities greatly vary across
heterogeneous urban environments.