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.

Methods
Data was generated from 16S rRNA sequencing from two sample types: organic matter contained in the tank of bromeliads (Tillandsia multicaulis) and from larvae of two fly taxa (Austrophorocera sp. and Copestylum sp.). Microbial reads were processed in QIIME2 and further analyses were conducted in R, using several packages.