Additional file 2 of Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals
Creators: name: Keller-Costa, T.
name: A. Lago-Lestón
name: J. P. Saraiva
name: R. Toscan
name: S. G. Silva
name: J. Gonçalves
name: C. J. Cox
name: N. Kyrpides
name: U. Nunes Da Rocha
name: R. Costa
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 1. Detailed Methodology. Sample processing and total-community DNA (TC-DNA) extraction. Extended Results. Features of the 16S rRNA gene-based taxonomic dataset and of metagenome assemblies subjected to functional analyses. Abundance distributions of bacterial classes across sample categories. Alpha-diversity in octocoral-associated and environmental prokaryotic communities. Extended discussion. Evidence for phylosymbiosis. Supplementary Figure S1. Photographs of the octocorals investigated in this study. (a) healthy Eunicella gazella, (b) Eunicella gazella branches with necrosis signs (black arrows), (c) healthy Eunicella verrucosa, (d) healthy Leptogorgia sarmentosa. (a, c and d) are underwater photographs of the octocorals in their natural habitat taken off the Algarve coast (South Portugal). Supplementary Figure S2. Class-level prokaryotic community profiles of healthy (EG_H) and diseased (EG_N) Eunicella gazella tissue, healthy Eunicella verrucosa (EV01 - EV04) and Leptogorgia sarmentosa (LS06 - LS08) specimens as well as seawater (SW01 - SW04) and sediment samples (SD01 - SD03). Relative abundances are displayed for taxa representing more than 1% of the total dataset reads. Taxa with abundances below 1% across the data are collectively labeled as ‘rare classes’. Supplementary Figure S3. Venn diagrams showing the shared and specific prokaryote phylotypes in octocorals and surrounding environments. (a, b) OTUs common and exclusive to seawater (blue), sediment (black) and healthy tissue of the octocorals Leptogorgia sarmentosa (olive), Eunicella verrucosa (orange) and E. gazella (salmon). (c, d) OTUs common and exclusive to seawater (blue), sediment (black) and healthy (salmon) versus necrotic (red) tissue of E. gazella. (a, c) Replicate samples were pooled to portray the total number of prokaryote OTUs within each sample category. (b, d) Only those OTUs present in all replicate samples of each sample category are shown. The following three OTUs were shared only between all octocoral samples while not consistently detectable in sediment and seawater: OTU_866 Endozoicomonadaceae; OTU_805 Shewanella bentica; OTU_943 Pseudoalteromonas porphyrae. Venn diagrams were created using the online tool InteractiVenn ( http://www.interactivenn.net/ [92]). Supplementary Figure S4. Abundance distributions of functional features enriched in the microbiomes of either healthy or necrotic Eunicella gazella tissue across the metagenomes of all octocoral species and seawater. Relative abundances of those Cluster of Orthologous Genes (COGs) of proteins in the microbiomes of the different octocoral species and seawater that were shown (in Figure 4) to be significantly enriched in the microbiomes of healthy (a) or necrotic (b and c) Eunicella gazella tissue. Bars represent average proportions (%) ± standard errors. If a given function was represented by more than one COG entry across the dataset, the proportions of these functionally belonging COGs were summed and the number of COGs that contributed to each bar chart is given below chart titles; if only one COG entry contributed to a chart, the respective COG ID is given. If data presented normal distribution (Shapiro-Wilk test) and equal variance (Brown-Forsythe test), One-way-ANOVAs followed by Bonferroni t-tests were used to check for significant differences between sample groups. If one of the assumptions was violated, Kruskal-Wallis tests on ranks were instead performed, followed by Dunn’s post-hoc tests. Statistical significance was established at P-values ≤ 0.05. Letters above error bars indicate significant differences (*P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001). Respective P-values are presented in the graphs. Panel (c) is equal to panel (b) but includes the necrotic E. gazella samples for an easier visualization of the “fate” of the respective functions in necrotic samples as compared to all healthy octocoral samples and seawater.