From Loh, T.-L., and Pawlik, J.R. (2014) PNAS. See paper for citations referred to below:
Study Sites. Surveys were conducted on coral reefs at 69 sites from 12 countries across the Tropical Northwestern Atlantic marine province (referred to herein as "Caribbean" for brevity) from 2008 to 2012. At each location, sponge community data and fish densities were recorded at 3-11 geographically distinct sites (>2 km apart) by a team of three to four that only included personnel from among the same five surveyors to minimize interobserver subjectivity. Transect lines were laid out along a contiguous section of the reef at 10-20 m (except for the shallow reefs off Bocas del Toro, Panama, and two sites off Key Largo, FL, 2-7 m).

From Loh, T.-L., et al. (2015) PeerJ:
Benthic Cover. At the same sites where fish abundance was counted, benthic community surveys were carried out by evenly placing a 1 × 1 m quadrat 5 times along each 20 m transect line, with 5 replicate transect lines laid end-to-end at similar depth, and a gap of 5 m between each transect (total of 25 quadrats per survey site). The benthos under 25 points within each quadrat were classified into the following categories: reef-building coral, sponge, fire coral (Millepora sp. C Linnaeus, 1758), gorgonian, zoanthid, other benthos, bare rock or dead coral, rubble, sand, silt, macroalgae (all erect species, but primarily Dictyota JV Lamouroux, 1809; Halimeda JV Lamouroux, 1812; Lobophora J Agardh, 1894; and Microdictyon spp. Decaisne, 1841), turfs (including cyanobacterial mats), and coralline algae. A total of 625 points were recorded at each survey site (Table S1). Coral-sponge interactions were quantified within the same number of quadrats along the same transect lines. For all coral colonies with at least 50% of their surface areas within each quadrat, we counted coral colonies in 3 categories: (1) those having no contact with sponges, (2) those that were growing adjacent to and in contact with sponges, and (3) those that were overgrown by sponges such that sponge tissue was covering live coral tissue.