Additional file 1 of Decline of a distinct coral reef holobiont community under ocean acidification
Creators: name: Williams, Jake
name: Pettorelli, Nathalie
name: Hartmann, Aaron C.
name: Quinn, Robert A.
name: Plaisance, Laetitia
name: O’Mahoney, Michael
name: Meyer, Chris P.
name: Fabricius, Katharina E.
name: Knowlton, Nancy
name: Ransome, Emma
Publisher: name: figshare
Year: 2024
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: Additional file 1: Table S1. Number of sequences retained at each step of denoising (implemented in DADA2); samples with fewer than 50,000 denoised sequences (ASVs) and duplicate samples were removed prior to analysis. Table S2. Effect size and significance of factors in PERMANOVAs describing the compositional differences among sites, and along the pH gradient for all multiomic data types; site fit as a blocking factor, except in the case of Halisarca sp. sponge fractions, which were only collected at one site. A p-value less than 0.05 indicates that the factor significantly affects composition. Bonferroni correction was applied to all PERMANOVA. Table S3. ASV estimated richness betta mixed model: fixed effects listed, random effect of locality. Model Explanatory Power: test statistic = 117.2, p&lt;0.05. A p-value less than 0.05 indicates that the explanatory variable significantly affects ASV richness. All values in the table are reported to two significant figures. Table S4. Phylum Shannon diversity betta mixed model: fixed effects listed, random effect of locality. Model Explanatory Power: test statistic = 3197.94, p&lt;0.05. A p-value less than 0.05 indicates that the explanatory variable significantly affects metabolite richness. All values in the table are reported to two significant figures. Table S5. ASV Shannon diversity betta mixed model: fixed effects listed, random effect of locality. R Squared (conditional)= 88.8%. A p-value less than 0.05 indicates that the explanatory variable significantly affects metabolite richness. All values in the table are reported to two significant figures. Table S6. Summary of tests and results for 16S rRNA gene and metabolomic data. Table S7. Compound richness linear mixed model: fixed effects listed, random effect of locality. R Squared (conditional)= 24.5%. A p-value less than 0.05 indicates that the explanatory variable significantly affects ASV richness. All values in the table are reported to two significant figures. Table S8. Compound Shannon diversity linear mixed model: fixed effects listed, random effect of locality. R Squared (conditional)= 32.0%. A p-value less than 0.05 indicates that the explanatory variable significantly affects ASV richness. All values in the table are reported to two significant figures. Fig. S1. Visual representation of read abundance from the ARMS 23S rRNA gene and 16S rRNA gene metabarcoding dataset. Data are aggregated across biological replicates to present the average composition of each fraction, at each pH, showing phylum (in white text) and class (in grey text). Fig. S2. NMDS of microbiome and metabolome composition of all fractions across the pH gradient, calculated using Morisita dissimilarity. Fig. S3. Microbial and chemical richness and Shannon diversity boxplots for all fractions across the pH gradient.