In tropical rainforests environmental conditions vary dramatically from the ground to the canopy, resulting in a marked stratification in the way vertical space is used by organisms, but research work is often limited to the understorey layer. Aerial insectivorous bats are a highly diverse group that plays key roles in the ecology of rainforests, but their use of vertical space remains elusive. Using automatic ultrasound recording stations placed in the canopy, subcanopy and understorey we tested if bat activity and species diversity are vertically stratified, both in the forest interior and near the edges of water bodies. These patterns were tested separately for individual species, and for two functional groups – open space and edge space bats. Insectivorous bat activity increased by roughly seven fold, and species diversity doubled, from the understorey to the canopy. Both edge space and open space bats were more active in the upper strata, but this tendency was much more accentuated in the latter. Myotis riparius was the only species with greater activity near the understorey. These patterns were altered at the edges of water bodies, where vertical stratification was much less marked. The observed patterns are parsimoniously explained by constraints imposed by vegetation clutter that change across strata, which affect bat species differently. Only bats better adapted to closed spaces are usually capable of foraging within the understorey, whereas the majority of species can exploit the free spaces immediately below the canopy; open space bats seem to concentrate their activity above the canopy. This importance of the inter strata open spaces for bat foraging highlights the need to preserve pristine stratified rainforests, as even selective logging usually disrupts vertical stratification. Moreover, the concentration of insectivorous bats at the upper strata of rainforests underlines the need to include canopy level sampling in ecological studies.

Tropical rainforests usually have multiple strata that results in a vertical stratification of ecological opportunities for animals. We investigated if this stratification influences the way bats use the vertical space in flooded and unflooded forests of the Central Amazon. Using mist-nets set in the canopy (17 to 35 m high) and in the understorey (0 to 3 m high) we sampled four sites in upland unflooded forests (terra firme), three in forests seasonally flooded by nutrient-rich water (várzea), and three in forests seasonally flooded by nutrient-poor water (igapó). Using rarefaction curves we found that species richness in the understorey and canopy were very similar. An ordination analysis clearly separated the bat assemblages of the canopy from those of the understorey in both flooded and unflooded habitats. Gleaning carnivores were clearly associated with the understorey, whereas frugivores were abundant in both strata. Of the frugivores, Carollinae and some Stenodermatinae were understorey specialists, but several Stenodermatinae mostly used the canopy. The first group mainly includes species that, in general, feed on fruits of understorey shrubs, whereas the second group feed on figs and other canopy fruits. We conclude that vertical stratification in bat communities occurs even within forests with lower canopy heights, such as Amazonian seasonally flooded forests, and that the vertical distribution of bat species is closely related to their diet and foraging behaviour.