Dataset: Microbiome data from sponges collected in 2013 and 2014 from reefs in Honduras, Belize, Panama and the Florida Keys.

Sponge collection:  Sponge species were collected from at least one site within four geographic regions spanning more than 15° of latitude (~1700 km) within the Caribbean Sea. Individual regions included the Bocas del Toro archipelago of Panama, the Miskito Cays of Honduras, the Mesoamerican barrier reef of Belize, and the Florida Keys. At each site, replicate small (3–5 ml) samples of dominant and conspicuous sponge species were collected by SCUBA using a dive knife and placed into individual bags containing seawater for transport back to the laboratory. Sponge samples always included a cross section with both inner and outer tissue regions to standardize collections and sample across the entire body of the sponge. Collections frequently included eight of the ten most dominant Caribbean species and species previously designated as both HMA and LMA sponges. Samples were preserved, processed, and prepared for δ13C and δ15N analysis. Sponges were identified to species and, if necessary, identities were verified via tissue histology and spicule preparations. Replicate subsamples of each sponge species were also preserved in 95% EtOH in 5 ml cryovials and frozen at −20 °C for analyses of microbial community structure.