Coral, water and sediment were sampled at 21 sites around the island of Mo'orea, French Polynesia in 2017, 2018, 2019, and 2020. Locations included Forereef on the oceanic side of the reef crest, Backreef on the lagoonal side of the reef crest, and Fringing Reef adjacent to the shoreline.

Coral: Individual corals from three species (Acropora hyacinthus, Porites lobata, and Pocillopora sp.) were tagged and repeatedly sampled twice a year in the rainy and dry seasons at depths between 1 and 10 meters water depth. Note that Pocillopora are a species complex on the Island of Mo'orea and while all individuals appeared to be Pocillopora meandrina, different species of this genus are morphologically indistinguishable at the size of these corals. Sampling was done free-diving or on SCUBA, with individual corals sampled using bone cutters (or chisels for P. lobata) that had been flame sterilized prior to each day's collection and were used only for that species to eliminate cross-species contamination. Corals with the same ID are the same individual sampled over time. All collections were done while wearing nitrile gloves. Upon return to the boat, coral fragments were placed in Zymo DNA/RNA shield and kept cold on Techni ice (frozen to -80 degrees Celsius) until processing.

Sediment: 2 milliliters (mL) of sediment were collected by gloved hands in sterile "snap-cap" vials. Upon return to the boat, samples were added to Zymo DNA/RNA shield and kept cold on Techni ice (frozen to -80 degrees Celsius) until processing.

Water: 500 mL of seawater was collected and kept chilled until it was filtered onto a 0.1 micron filter, then put into Zymo DNA/RNA shield and kept cold on Techni ice (frozen to -80 degrees Celsius) until processing.

Sample processing:
Initial processing included bead beating of all samples prior to them being frozen at -80 degrees Celsius and shipped back to either Rice University or Oregon State University. Coral and sediment were extracted using the ZYMO quick-DNA extraction kit and water samples with Qiagen Powerwater DNA extraction kit. DNA was amplified (at OSU) following the Earth Microbiome Project protocols, using the updated primers of 515f (Parada et al. 2016) and 806r (Apprill et al. 2015). Due to co-amplification of eukaryotic 12S rRNA genes, DNA was size selected using Blue Pippin (Sage Scientific) prior to sequencing to minimize 12S sequence generation. Sequencing was performed on the Illumina MiSeq platform using the V.2 chemistry at the Center for Genome Research and Biocomputing at Oregon State University. While we used forward and reverse barcoding for sequencing, reverse read quality scores were not acceptable and only forward reads were used and uploaded to the SRA. In certain cases, there were repeated sequencing runs for individual samples. That is indicated with different numbers.

Accession numbers of DNA sequences generated as part of this project are archived and available in the National Center for Biotechnology Information (NCBI) Short Read Archive under BioProject Identifier PRJNA684406 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA684406).