Microecosystem models could allow understanding of the impacts of pollutants such as polycyclic aromatic hydrocarbons on ecosystem functioning. We studied the effects of atmospheric phenanthrene (PHE) deposition on the microecosystem "moss/soil interface-testate amoebae (TA) community" over a 1-month period under controlled conditions. We found that PHE had an impact on the microecosystem. PHE was accumulated by the moss/soil interface and was significantly negatively correlated (0.4 < r 2 < 0.7) with total TA abundance and the abundance of five species of TA (Arcella sp., Centropyxis sp., Nebela lageniformis, Nebela tincta and Phryganella sp.). Among sensitive species, species with a superior trophic level (determined by the test aperture size) were more sensitive than other TA species. This result suggests that links between microbial groups in the microecosystems are disrupted by PHE and that this pollutant had effects both direct (ingestion of the pollutant or direct contact with cell) and/or indirect (decrease of prey) on the TA community. The TA community seems to offer a potential integrative tool to understand mechanisms and processes by which the atmospheric PHE deposition affects the links between microbial communities.