Sampling:
Daily trips were made to the sampling sites using small boats. Start and end dates of field missions:
March 28 - April 17, 2022
September 1 -& October 4, 2022
February 21 - April 13, 2023

Both apparently healthy and actively diseased colonies of Agaricia agaricites (14 diseased, 27 healthy), Acropora cervicornis (6 healthy), Colpophyllia natans (19 diseased, 20 healthy), Diploria labyrinthiformis (7 diseased, 19 healthy), Montastraea cavernosa (18 diseased, 20 healthy), Orbicella annularis (18 diseased, 24 healthy), Porites astreoides (8 diseased, 32 healthy) were sampled for various analyses. All work was completed by divers on SCUBA. Each sampled colony was marked for relocation by hammering a numbered cattle tag into the adjacent dead substrate and then photographed from above. Then, using either a hammer and chisel or underwater Nemo drill with a diamond tipped hole saw (no anvil), coral fragments approximately 4 x 4 centimeters (cm) were collected from each colony. Three fragments were collected from apparently healthy corals (HH), and six fragments from diseased corals, including three fragments immediately adjacent to the lesion boundary (DD) and three fragments from apparently healthy tissue (HD). All fragments were placed into individually labeled whirlpacks and transported to the surface. Sample scar edges on the sampled colonies were sealed with natural clay. Corals were rephotographed before and after sealing with the clay. Marked colonies were mapped using a camera time-paired to a GPS on a float that was towed above by the sampler. Once at the surface, one fragment from each sample type (HH, HD, DD) was processed for microbial analyses, gene expression, TEM, and histopathology (separate data sets).

Monitoring:
Using maps created using the GPS-paired images, divers on SCUBA relocated colonies, if possible. Colonies that were found were rephotographed, and the following was recorded: size estimates (length, width, and height), percent of the colony showing old mortality (defined as calyx degradation and algal recruitment), percent of the colony showing recent mortality (defined as bright white exposed skeleton with no algal recruitment), percent of living tissue that was bleached or paled, and disease identification (if applicable). Colony ID was confirmed by comparing monitoring photos to photos of the colony at sampling. All tissue was sampled from 15 of the 233 sampled colonies, and therefore these corals were not reassessed. At six months post-sampling, 159 corals were found, photographed, and monitored for health status. At one year post-sampling, 146 corals were found, photographed, and monitored for health status.

Instrument Details:
Corals were tagged with 2½ inch masonry nails and plastic cattle tags with unique IDs. Coral and sample-specific images were recorded with Olympus Tough TG-6 cameras in Olympus underwater housings. Either Milwaukee 3lb sledges and ¾ inch mason chisels or Nemo underwater drills with 1½ inch diamond hole saws (anvil removed) were used to collect fragments.