Dataset: Microbe priority experiment counts

A priority experiment was conducted in 24 recirculating tanks at the Smithsonian stations in Bocas del Toro, Panama. Replicate staghorn corals fragments from 10 genotypes were placed into the tanks containing 12 liters of UV sterilized seawater. Twelve tanks were then exposed to an antibiotic cocktail of Kanamycin, Ampicillan, Tetracycline and Choloramphenicol (100mg/ml each) twice over a 48hr period, and the corals from the antibiotic treated and untreated tanks were sampled for DNA (T0 sample point) and lesioned with an airbrush. Half of the antibiotic- treated and untreated tanks were then exposed to 30ml of disease slurry (D) or healthy slurry (H) for the first exposure. 24hrs later a second dose of disease or healthy slurry was applied to complete the priority experiment treatments of healthy_healthy (h_h), disease_disease (d_d), healthy_disease (h_d), and disease_healthy (d_h). DNA for the microbial analyses were sampled 18hrs later (T2) and then disease was monitored over the course of the experiment. Corals that developed disease were sampled (T3) and sacrificed. All of the corals were sampled (T3 timepoint) on day 7.

DNA from preserved coral samples were extracted using an Agencourt DNAdvance kit, in order to prepare 16S rDNA profiling libraries. 16s libraries of the hypervariable V3_v4 region were then prepared using a two-step PCR protocol and combinatorial barcodes, resulting in amplicon lengths from ~300-400 bp paired-end joined sequences from Illumina 250 bp sequencing on an Illumina HiSeq 2500.

16s sequencing data were clustered into operational taxonomic units (OTUs) using a 97% identity threshold in QIIME. Default QIIME settings were used to align reads, to remove chimera sequences, and to assign taxonomy.