Data for analyzing the microbiome of bromeliads and fly larvae inhabiting the tropical cloud forest of Mexico

Background. The tropical montane cloud forest contains high levels of
epiphyte diversity. Epiphytic tank bromeliads play an important role in
the functioning of these ecosystems and provide a microhabitat for many
species of invertebrates. Microbial ecology theory suggests that the
environment serves as a source of microbes for animals, but the
contribution of this factor to the composition of an animal microbiome
varies. In this study, we examined the extent to which tank bromeliads
(Tillandsia multicaulis) serve as a source of microbes for fly larvae in a
cloud forest fragment in central Veracruz, Mexico. Methods. We used 16S
rRNA sequencing to characterize the bacterial communities in the organic
matter within bromeliad tanks and in the whole bodies (surface and gut) of
larvae from two fly taxa (Austrophorocera sp. and Copestylum sp.) that
inhabit these bromeliads. To assess the contribution of bromeliads to the
microbiome of the fly larvae, we conducted fast expectation-maximization
microbial source tracking (FEAST) analysis. Results. The bacterial
communities in bromeliad tanks were primarily composed of Pseudomonadota,
Acidobacteriota, Bacteroidota, Verrucomicrobiota, and Spirochaetota.
Similarly, communities of the fly larvae contained Pseudomonadota,
Bacteroidota, Bacillota, and Actinomycetota. Bromeliad tanks exhibited the
highest bacterial richness, followed by Copestylum and Austrophorocera
larvae. Beta diversity analyses indicated that bacterial communities
clustered by species. We found a modest contribution of bromeliads to the
fly microbiome, with nearly 30% of the larvae microbiome originating from
the organic matter deposited in the tanks. Conclusions. Our data suggest
that the microbiome of Diptera larvae, which inhabit tank bromeliads
during their larval stage, is nourished to some extent by the bacterial
communities present in the organic matter within the tank.