Additional file 1 of Synthesis of recovery patterns in microbial communities across environments

Additional file 1: Supplementary methods. Literature Search and model descriptions. Table S1. Accession numbers and links to all sequences reused in this work and their processing parameters. Table S2. Slope estimates for models comparing immediate changes in dispersion following disturbance, calculated on Bray–Curtis values and null model outputs. Figure S1. Proportion of reads preserved after quality filtering (a), chimera checking (b), and selection of bacterial reads (c). Figure S2. Models fit to data standardized across studies and to data standardized within studies yield very similar parameter estimates. Each panel shows the fixed effect estimates for models fit to (a) richness before-after disturbance, (b) richness change through time following disturbance, (c) dispersion before-after disturbance, (d) dispersion (z-score) before-after disturbance, (e) dispersion change through time following disturbance, (f) dispersion (z-score) change through time following disturbance, (g) turnover change through time following disturbance, and (h) turnover (z-score) change through time following disturbance. Figure S3. Posterior distributions of the immediate response in richness to disturbance, separated by disturbance type and microbial realm. Figure S4. The immediate effect of a disturbance on richness was only related to the rate of recovery of richness in mammals. Figure S5. Slope and interval estimate of richness (Hill q0, purple) and inverse Simpson’s index (Hill q2, blue) immediately following disturbance (a) and over time (b). Figure S6. The effect of disturbance on microbiome dispersion, immediately (< 4 days) after disturbance (a), and over 50 days of recovery (b). Figure S7. Posterior distribution of temporal response of dispersion to disturbance, separated by disturbance type and microbial realm. Figure S8. Posterior distribution of temporal response of turnover to disturbance, separated by disturbance type and microbial realm. Figure S9. The effect of disturbance on turnover. Figure S10. Relationships between the immediate effect of a disturbance on richness and a microbiome’s long-term recovery of composition vary among environments.