Statistical Analysis
Statistical analyses were conducted using PRIMER v7 plus PERMANOVA,
Statistical Analyses of Metagenomic profiles (STAMP) software (Parks et
al. 2014), and R (R Project for Statistical Computing). Significant
differences in the relative abundances of microbial genera and functions
in the coral microbial communities sampled from inner and outer reefs
were identified by permutational multivariate analysis of variance
(PERMANOVA) using Bray-Curtis distances of normalized relative abundance
obtained using a square-root transformation. A cluster analysis was
created to visualize the similarity of the coral microbiome between
temperature treatments. We also used PRIMER to calculate Pielou’s
evenness index (J’) and Shannon’s diversity index (H’) of microbial
genera. Principal Component Analyses (PCA) and the multiple comparisons
of either taxa or functions across the three groups of metagenomes
(i.e., pre-treatment, ambient, and heat) were conducted in STAMP using
ANOVA/Tukey-Kramer, Welch’s pairwise comparisons, and Benjamini-Hochberg
FDR corrections. We used R to test parametric assumptions of normality
(Shapiro-Wilk’s test) and homoscedasticity (Bartlett’s test), and
differences in the percent changes of maximum photochemical efficiency
of photosystem II (Fv/Fm) and productivity to respiration ratios (GP: R)
between temperature treatments (Student’s T-Test).