Figure 6. The immediate effect of a disturbance is not related to the microbiome’s long-term compositional recovery.
LEGENDS
Figure 1. Measuring microbial recovery after disturbance. Community richness can be measured before disturbance (yellow), immediately after disturbance (green), and over longer time periods (blue, a). Compositional dynamics can be assessed using compositional dissimilarity metrics (i.e., Bray-Curtis, b). Dispersion can be measured as the pairwise dissimilarity between experimental replicates, and turnover can be measured as the pairwise dissimilarity between pre-disturbance and disturbed communities (red). Following disturbance, communities dispersion can increase or decrease over time if communities become more or less dissimilar, respectively (c). They may also return to their pre-disturbance composition (negative turnover trend) or become increasingly dissimilar from the pre-disturbance community (positive turnover trend) Insets are the relationship between time (x-axis) and turnover (dashed line, y-axis) or dispersion (solid line, y-axis).
Figure 2. Samples used in this synthesis. We selected time series that had control samples and multiple samples after disturbance (a). A vertical black line denotes a disturbance event in all cases; samples taken on the day of disturbance (before or after) are shown along this line. A vertical grey line indicates the fourth day after disturbance. Studies which had not sampled the recovering microbiome within <4 days after disturbance were excluded from assessments of the immediate impacts of disturbance on richness and dispersion. All samples were standardized to 1,500 observations per sample, and had an average coverage >0.9 (b).
Figure 3. The effect of disturbance on microbiome richness, immediately (<4 days) after disturbance (a), and over 50 days of recovery (b). Richness was calculated as the number of observed taxa in each sample, and is presented with a log2-transformed y-axis. Circles represent samples, and are colored by study. In a, solid black circles indicate the mean across time series per environment with a 95% CI indicated by error bars. In b , regression lines for each time series are colored by study, and the solid black line shows the mean response across time series per environment. The 95% CI is displayed as a grey shaded area, and environments for which overall trends deviate from zero are indicated with an asterisk (*) on the bottom right corner.
Figure 4. Consistent effect of disturbance on microbiome dispersion are not detected, immediately (<4 days) after disturbance (a), or over 50 days of recovery (b). Dispersion was calculated as the pairwise Bray-Curtis distance between replicates for each time point within each time series, and each circle is a pairwise comparison, colored by study. In a, solid black circles indicate the mean across time series per environment with a 95% CI. In b , regression lines for each time series are colored by study, and a solid black line indicates the mean response across time series per environment. The 95% CI of the overall response in each environment is displayed as a grey shaded area. y-axis scales differ per environment, and the overall trends from each environment did not deviate from zero.
Figure 5. The effect of disturbance on community recovery is environment-dependent. For each time series, recovery was calculated as the pairwise distance between post-disturbance samples and pre-disturbance controls. Each point is a pairwise comparison, colored by study. recover to increasingly different conformations Regression lines for each time series are colored by study, and a solid black line indicates the mean response across time series per environment. The 95% CI is displayed as a grey shaded area, and environments for which overall trends deviate from zero are indicated with an asterisk (*) on the bottom right corner.
Figure 6. The immediate effect of a disturbance is not related to the microbiome’s long-term compositional recovery. Each point is a time series, colored by its environment. Immediate richness responses were calculated as the effect of disturbance on community richness (Figure 3a), and log-transformed. Turnover rates were calculated as the slope estimate for turnover over time. Error bars show the 95% CI for both metrics. Large circles indicate the mean response per environment.