Coral SML microbiome
The metagenomes associated with the coral SML of P. strigosa  were sequenced at high coverage, ranging from 356,426 to 1,296,198 sequence counts (Supplemental Tab. 1). Principal Component Analyses of bacterial genera and genes related to stress response, nitrogen metabolism, and sulfur metabolism (Fig.1), showed that dispersion (β-diversity) was lower among metagenomes from heat-stressed corals than from pre-treatment and control groups. Pairwise PERMANOVAs concluded that relative abundances of microbial genera (t = 2.62, P(perm) < 0.03), nitrogen metabolism genes (t = 2.52, P(perm) = 0.03), and sulfur metabolism genes (t = 3.14, P(perm) = 0.03) were significantly different between pre-treatment and heat-stressed microbiomes. Metagenomes from corals at ambient conditions did not significantly change when compared to pre-experiment or heat treatments. Relative abundances of microbial stress response genes showed no significant change across treatments.
Heat exposure led to a significant increase in the relative abundances of Ruegeria (t = - 2.38, corrected p-value < 0.02),Roseobacter (t = - 2.15, corrected p-value < 0.001),Oceanibulbus (t = - 1.58 corrected p-value < 0.03),Chromohalobacter (t = - 0.84, corrected p-value < 0.02), and Halomonas (t = - 0.87, corrected p-value < 0.02), according to Welch’s pairwise comparisons among the top 20 most abundant taxa in the coral microbiome (Fig. 2). In contrast, there was a significant decrease in the relative abundances of Shewanella (t = 0.82 corrected p-value < 0.001), Synechococcus (t = 0.88, corrected p-value < 0.04), and Vibrio (t = 0.284, p-value < 0.02) in the microbiome of corals exposed to heat treatment (Fig. 2). Heat-stressed coral SML metagenomes analyzed at the level of bacterial genera formed a cluster with the greatest similarity (Bray-Curtis index > 95%) across all samples (Supplemental Fig. 2). Microbial richness (S, number of genera) ranged from 578 to 587 genera and did not significantly change between microbiome samples collected in situ and across the experimental treatments (Supplemental Tab. 2). Diversity (H’) was highest in situ due a decrease in evenness (J’) under experimental conditions.
Within nitrogen metabolism, the relative abundances of microbial gene pathways related to amidase with urea and nitrile hydratase (t = - 0.363, corrected p-value < 0.0001), allantoin utilization (t = - 1.079, corrected p-value = 0.042), and nitrogen fixation (t = - 0.130, corrected p-value = 0.049) increased in the coral microbiome under heat stress, while nitrosative stress (t = 1.628, corrected p-value = 0.033), and ammonia assimilation (t = 4.51 corrected p-value = 0.037) decreased (Fig. 4.B).
Sulfur metabolism microbial genes also changed in relative abundance after heat exposure of corals. There was an increase in glutathione utilization (t = - 1.70, corrected p-value < 0.0001), sulfur oxidation (t = - 8.08, corrected p-value < 0.0001), and taurine utilization (t = - 1.44, corrected p-value < 0.0001), and a decrease in inorganic sulfur assimilation (t = 8.04, corrected p-value < 0.0001) (Fig. 4.C).