Height from the ground and phytotelm pH affect prokaryotic diversity in epiphytic bromeliads

O'Reilly-Berkeley, Xaali 1 2 3 ; Hughes, Thomas D.3 4; Mossman, Hannah3; Rowntree, Jennifer K.3 4 ; Preziosi, Richard F.3 4

Published Sep 23, 2026 on Dryad. https://doi.org/10.5061/dryad.sf7m0cgm5

Data files

Sep 23, 2026 version files 13.48 MB

Abstract

The presented data is the result of metabarcoding and sequencing of eDNA from the phytotelmata of epiphytic bromeliads in the rainforests of San José de Payamino, in the Ecuadorian Amazon. The dataset includes the data from QIIME (.qza) and the metadata. The field work for this project was carried out with permission from the former Ministry of the Environment of Ecuador (Ministerio del Ambiente, MAE) and in collaboration with the Ecuadorian national biodiversity institute (Instituto Nacional de Biodiversidad, INABIO), under the research permit number MAE-DNB-CM-2016-0045. This work was carried out in accordance with the formal agreement between the San José de Payamino Community and the Timburi Cocha Research Station.

Dataset DOI: 10.5061/dryad.sf7m0cgm5

Description of the data and file structure

Detailed description of the methods can be found in O'Reilly-Berkeley et al. "Habitat and plant characteristics affect prokaryotic diversity in epiphytic bromeliad phytotelmata". Briefly, sterile swabs were rubbed on the base of interior leaves of the central phytotelm of each bromeliad before plant and invertebrate collection. The swabs were preserved in cryogenic tubes and placed in liquid nitrogen until DNA extraction. The V4 region of the 16S ribosomal unit was amplified. Following library preparation detailed in the associated manuscript, libraries were sequenced. Sequencing data was analysed with QIIME Deblur prior to import into R for statistical analyses using mostly phyloseq and vegan packages.

Files and variables

File: Bac_metadata_expanded.txt

Description: Metadata for the bromeliad from which the samples were collected

Variables

sample-id: ID of each sample, including technical replicates
name: Number associated to the bromeliad identifier
bromeliad: Bromeliad identifier
site: Collection site
material: How the sample was taken
height: Height at which the bromeliad was found on the tree
ph: pH of the central phytotelm of the bromeliad
phytotelmt: Temperature of the central phytotelm of the bromeliad
volume: Potential capacity (ml) of the whole bromeliad phytotelmata put together
longestleaf: Longest leaf (cm) of the bromeliad
nleaves: Number of leaves on the bromeliad
basecirc: The circumference (cm) around the base of the bromeliad
season: The sampling seasion
forest: The forest type, primary or secondary

File: Bac_rep_seqs.qza

Description: Representative sequences

File: Bac_table-deblur.qza

Description: OTU table

File: Bac_taxonomy_pretrained.qza

Description: The pre-trained taxonomy

File: Bac_rooted-tree-copy.qza

Description: The rooted phylogeny

Code/software

The data can be imported to R using the qiime2R package, available as follows:

devtools::install_github("jbisanz/qiime2R")

library('qiime2R')

To then compile a phyloseq object, use the following code:

Bac_physeq<-qza_to_phyloseq(features="Bac_table-deblur.qza", tree="Bac_rooted-tree-copy.qza", taxonomy="Bac_taxonomy_pretrained.qza", metadata = "Bac_metadata_expanded.txt")