Additional file 2 of Destabilization of mutualistic interactions shapes the early heat stress response of the coral holobiont

Supplementary Material 2. Supplementary tables: Table S1. One ASV was identified as contaminant using the R package decontam ( https://github.com/benjjneb/decontam ). Table S2. Generalized linear mixed models tested the fixed effect of treatment (ambient, heat), time (T0, T1, T2, T3, T4, Tp, T5), colony of origin (A, B, C) and the interaction between treatment and time on: health score, photosynthesis (P; sqrt-transformed), respiration (R; absolute), Gross P:R and photochemical effective efficiency (sqrt-transformed) in the coral Porites lutea. Tank and fragment were included in the model to account for repeated measures. The pairwise comparisons (Šidàk correction) for significant interactions are reported here. Estimates are not back-transformed. Significant factors (p < 0.05) are indicated in bold. Table S3. (separate Dataset file). Summary of sequencing statistics of the transcriptomic dataset, and percentage of reads mapping to the reference genomes. Table S4. (separate Dataset file). Outcome of the Gene Ontology (GO) enrichment analyses (Biological Processes) for the coral host between low stress (< 1 DHW) and ambient conditions; only significant genes (adjusted p < 0.05) are shown. Table S5. (separate Dataset file). Outcome of the Gene Ontology (GO) enrichment analyses (Biological Processes) for the coral host between moderate stress (3 DHW) and ambient conditions; only significant genes (adjusted p < 0.05) are shown. Table S6. (separate Dataset file). Overview of the coral host Differentially Expressed Genes (DEGs) detected between moderate stress (3 DHW) and ambient conditions. Table S7. (separate Dataset file). Overview of the coral host gene expression under moderate stress (3 DHW) compared to ambient conditions, shown as log-fold-changes (logFC). The dataset excludes Differentially Expressed Genes (DEGs), as listed in Table S6. Table S8. (separate Dataset file). Overview of the discriminative coral host genes selected through multilevel sPLS-DA analysis. Table S9. (separate Dataset file). Outcome of the Gene Ontology (GO) enrichment analyses (Biological Processes) for the coral-associated Symbiodiniaceae between low stress (< 1 DHW) and ambient conditions; only significant genes (adjusted p < 0.05) are shown. Table S10. (separate Dataset file). Outcome of the Gene Ontology (GO) enrichment analyses (Biological Processes) for the coral-associated Symbiodiniaceae between moderate stress (3 DHW) and ambient conditions; only significant genes (adjusted p < 0.05) are shown. Table S11. (separate Dataset file). Overview of Symbiodiniaceae Differentially Expressed Genes (DEGs) detected between low stress (< 1 DHW) and ambient conditions. Table S12. (separate Dataset file). Overview of Symbiodiniaceae Differentially Expressed Genes (DEGs) detected between moderate stress (3 DHW) and ambient conditions. Table S13. (separate Dataset file). Overview of the discriminative Symbiodiniaceae genes selected through multilevel sPLS-DA analysis. Table S14. Permutation multivariate analysis of variance (adonis function in R vegan package) based on Bray–Curtis dissimilarities applied on square-root-transformed relative abundances to examine the effects of sample type (fixed, three levels: “coral”, “seawater”, “feed”) on the microbiome. P-values were calculated using 10,000 permutations and statistical significance (p < 0.05) is shown in bold. Table S15. Permutation multivariate analysis of variance (adonis function in R vegan package) based on Bray–Curtis dissimilarities applied on square-root-transformed relative abundances to test the effect of time (fixed, six levels: “T0”, “T1”, “T2”, “T3”, “T4”, “T5”), treatment (fixed, two levels: “ambient”, “heat”) and colony of origin (fixed, three levels: “A”, “B”, “C”) on the coral microbiome. Tank was also fitted in the model. P-values were calculated using 10,000 permutations and statistical significance (p < 0.05) is shown in bold. Table S16. A linear mixed model (gaussian) testing the effect of treatment (fixed, two levels: “Ambient”, “Heat”) time (fixed, six levels: “T0”, “T1”, “T2”, “T3”, “T4”, “T5”) and colony of origin (fixed, 3 levels) on the Shannon diversity index of the coral microbiome (rarefied data). Tank was included in the model as random effect. Statistical significance (p < 0.05) is shown in bold. Table S17 (separate Dataset file). Overview of the 88 highly correlated variables across datasets identified through DIABLO analyses.