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1 Supplementary Information Table S1. Per-sample sequences, observed OTUs, richness estimates, diversity indices and coverage. Samples codes as follows: YED (Young leaves Endophytes), MED (Mature leaves Endophytes), YEP (Young leaves Epiphytes), MEP (Mature leaves Epiphytes), N (Necromass), R (Roots). Asterisks indicate significant differences compared to the other samples (p < 0.05). SE (Standard Error). Sample Total Sequences Observed OTUs Richness Diversity Coverage S CHAO(SE) Raw Raw Gini- Shannon- Simpson Weaver Index Index C GOOD YED1 25, (43.03) YED2 8, (46.93) YED3 28, (29.73) MED1 14, (35.27) MED2 10, (40.88) MED3 6, (46.55) YEP1 68, (33.93) YEP2 58, (40.16) YEP3 57, (26.04) MEP1 53, (34.14) MEP2 51, (43.76) MEP3 23, (49.53) N1 56, (35.08)* N2 102, (29.84)* N3 71, (33.80)* R1 71, (24.52)* R2 66, (33.44)*
2 Figure S1. OTU-accumulation curves at 3% distance cutoff. Samples were collected from different tiers of the plant (YED Young Endophyte; MED Mature Endophyte; YEP - Young Epiphyte; MEP Mature Epiphyte; N Necromass; R Root).
3 Figure S2. Rank abundance plot of OTUs observed at 97% similarity in datasets of Espeletia sp. amplicons, based on sequence abundance for each sample. (YED Young Endophyte; MED Mature Endophyte; YEP - Young Epiphyte; MEP Mature Epiphyte; N Necromass; R Root).
4 Figure S3. Raw abundance of taxa belonging to the core community of Espeletia plants. Data is divided into phyla and different colors represent different genera. (YED Young Endophyte; MED Mature Endophyte; YEP - Young Epiphyte; MEP Mature Epiphyte; N Necromass; R Root).
5 Figure S4. Hierarchical Clustering analysis using Weighted UniFrac distances. (YED Young Endophyte; MED Mature Endophyte; YEP - Young Epiphyte; MEP Mature Epiphyte; N Necromass; R Root).
6 Figure S5. Pairwise community comparisons based on differentially abundant OTUs. X axis represents the phylum of each OTU and the Y axis the Log2 fold change of the first community vs the second. OTUs are colored according to their respective class. All differences are statistically significant (p < 0.01).
7 Figure S6. Predicted metabolic pathways present in the microbiome associated with Espeletia sp. using PICRUSt. The inner circles represent the metabolic categories as classified in the KEGG database. The heat map represents the predicted abundances for the metabolic pathways inside the categories where red indicates increased predicted abundance. (YED Young Endophyte; MED Mature Endophyte; YEP - Young Epiphyte; MEP Mature Epiphyte; N Necromass; R Root).
8 Figure S7. General relative abundance of genes involved in several metabolic pathways. The signal intensity was normalized by the mean intensity of the microarray. Mean values of samples were plotted for mayor gene categories. (YED Young Endophyte; MED Mature Endophyte; YEP - Young Epiphyte; MEP Mature Epiphyte; N Necromass; R Root).
9 Figure S8. Mean normalized signal intensity of carbon-fixation genes clustered by major functional processes: 3-Hydroxypropionate cycle, 3-Hydroxypropionate/4-Hydroxybutyrate cycle, Calvin cycle, Dicarboxylate/4-Hydroxybutyrate cycle, Reductive Acetyl CoA Pathway, Reductive Tricarboxylic Acid cycle, Carboxysome, Methane oxidation and Methanogenesis. The signal intensity was normalized by the mean intensity of the microarray. Mean values of samples were plotted with their respective SE. Variations among communities were tested with one-way ANOVA and letters indicate statistically significant differences (p < 0.05). Pairwise testing was corrected using Tukey s post-hoc test, letters represent statistically significant groups. (YED Young Endophyte; MED Mature Endophyte; YEP - Young Epiphyte; MEP Mature Epiphyte; N Necromass; R Root).
10 Figure S9. Mean normalized signal intensity of genes involved in remediation of organic compounds clustered by major compounds: Aromatics, chlorinated solvents, herbicides, other organic compounds, pesticides and polycyclic aromatics. The signal intensity was normalized by the mean intensity of the microarray. Mean values of samples were plotted with their respective SE. Variations among communities were tested with one-way ANOVA and letters indicate statistically significant differences (p < 0.05). Pairwise testing was corrected using Tukey s post-hoc test, letters represent statistically significant groups. (YED Young Endophyte; MED Mature Endophyte; YEP - Young Epiphyte; MEP Mature Epiphyte; N Necromass; R Root).
11 Figure S10. GeoChip predicted nitrogen metabolic transformations present in Espeletia sp. microbial communities. Colors in gene names indicate the sample where such gene was relatively more abundant. Outer ring indicates the total relative abundance of genes involved in nitrogen transformations. (YED Young Endophyte; MED Mature Endophyte; YEP - Young Epiphyte; MEP Mature Epiphyte; N Necromass; R Root). Colors in gene names indicate the sample in which the gene was more abundant.
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