Sampling and analytical procedures:
Corals of two species (Pocillopora cf. meandrina and Acropora hyacinthus) were collected from the reef crest on the north side of the island of Mo'orea, French Polynesia (GPS location: 17.47541 S, 149.8402 W). The fragmented corals were transported to Gump Research Station where they equilibrated for >24 hours in shaded flowing seawater tables.

Coral fragments were exposed to slightly elevated bicarbonate (+1 mM) and Ammonium (0.5 mM NH₄) for 24 hours prior to being sampled (T0 controls) and then exposed to various experimental treatments to better understand the response of reefs to factors that trigger viral outbreaks.

Treatments were:

Control: no modification
Nutrient: addition of two millimolar nitrate (2mM NO₃)
Temperature: increase of 3 degrees Celsius (+3°C)
Coral exudate: addition of a mean of 2 millimolar dissolved organic carbon (DOC) + particulate organic carbon (POC) from a bleaching coral (co-occurring con-specific coral head
Exudate: exudate blank is the coral exudate only, with no coral sample added.
Blank: water with no coral added

Note: Water was filtered (0.2 micron filtration) before being used in the experiment.

Corals were kept in individual recirculating water baths. Fragments from a single coral head were exposed to all treatments, with replicate samples of the same coral head sharing the same letter designation. At specified time points (6,12, 24, and 48 hours since exposure to treatment began) corals were sacrificed and water from the water baths (microcosm water) was sampled for microbial community composition by filtering ca. 0.5L water through a 0.2 micron filter (Sterivex-GP 0.22 µm, SVGP01050, Millipore) after which they were frozen.

Coral exudate blank clogged the Sterivex filter, resulting in a marked decrease in the amount of water that was filtered. Coral pieces were placed in Zymo DNA/RNA shield. Initial processing of the corals included bead beating and then freezing at -80°C, followed by shipping to either Rice University or Oregon State University (OSU) for DNA extraction.

DNA sequencing
DNA was extracted using either the Zymo quick-DNA extraction kit (corals) or the Quigen Powerwater kit (water samples) following manufacturer protocols. 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 sequencing. While we used dual indexed primers during sequencing, reverse read quality scores were not acceptable and only forward reads were used and uploaded to the Sequence Read Archive (SRA).

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.

All data associated with this submission has been made available through the NCBI Short Read Archive under BioProject PRJNA684406 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA684406). The accompanying data files list the accessions numbers and sampling information.

Sample ID/ Library ID details:
B = blank
C = control
V = exudate
VB = exudate blank
N = nutrient
T = temperature
ACR = Acropora
POC = Pocillopora

"Vd-12_water_Experiment_d" means Exudate, replicate d, 12 hours into treatment, water experiment, replicate d

"ACR-Cb-0-20_b2" means Acropora, Control, replicate b, zero time (0 hours into treatment), sequential sample number 20, replicate b2

"POC-Cc-0-44_c3" means Pocillopora, Control, replicate c, 0 hours into treatment, sample number 44, replicate c3