ITS of Galaxea fascicularis: coral fragment
To ensure that the community would be representative for the whole coral polyp, each frozen polyp was homogenized with a frozen mortar and pestle and 40 mg of the homogenized materials were used for DNA extraction. Note the coral bacterial community was inclusive of bacteria from coral tissue, mucus, skeleton and in hospite Symbiodiniaceae. For Symbiodiniaceae community characterization, the partial 5.8S, entire ITS2 and partial 28S rDNA genes were amplified using the primer pair: Sym_Var_5.8S2 [5 GTGACCTATGAACTCAGGAGTCGAATTGCAGAACTCCGTGAACC 3] (Hume et al. 2015); Sym_Var_Rev [3 CTGAGACTTGCACATCGCAGCCGGGTTCWCTTGTYTGACTTCATGC 5] (Hume et al. 2013) (Illumina adapters underlined). For bacterial communities, hypervariable regions V5-V6 of the 16S rRNA gene were amplified using the primer pair 784F (5 GTGACCTATGAACTCAGGAGTCAGGATTAGATACCCTGGTA 3) and 1061R (5 CTGAGACTTGCACATCGCAGCCRRCACGAGCTGACGAC 3) (Illumina adapters underlined). DNA extraction, PCR amplification (in triplicate) and library preparation was conducted following established protocols (16S (Chan et al. 2019), ITS2 (Chan et al. 2023); Supplementary methods S1), including 3 DNA extraction blanks and 3 PCR negative controls. The libraries were sequenced at the Walter and Eliza Hall Institute (Melbourne, Australia) in one Illumina MiSeq run using the v3 reagents (2  300 bp).