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. 2016 Aug 30;82(18):5530–5541. doi: 10.1128/AEM.01327-16

FIG 2.

FIG 2

Shifts in taxonomy through time by microbiome type. (a) Bubble plots showing the mean relative abundances of the most abundant phyla and the 20 most abundant Actinobacteria OTUs (across week 0 and week 6 combined) by microbiome type. Bubbles are shown for the initial inocula, week 0 (pre-crude oil), and week 6 (post-crude oil). Actinobacteria are highlighted to indicate that this phylum converged strongly by week 6 across microbiome types and was by far the dominant bacterial group. The abundance of Actinobacteria at week 6 did not differ significantly across microbiome types, while those of all other phyla and genera shown did (P < 0.05; multiple ANOVA with P value correction using the Benjamini-Hochberg false discovery rate). (b) Dot plot with 95% confidence intervals showing changes in OTU abundance from week 0 to week 6 for each microbiome type. The OTUs displayed are those with a relative abundance that increased significantly between time points by at least 1% in at least one microbiome type. The abundance of each OTU for each microbiome type at week 0 is indicated in a bar plot at the bottom of the figure. (c) Ternary plots of OTUs shared between all three microbiome types and across all time points to demonstrate treatment fidelity over time. The relative abundance of each OTU across microbiome types was normalized to 1 at each time point, so that the comparison represents the abundance of an OTU in relation to those of the other microbiome types, as opposed to other OTUs within a microbiome type. Colors represent the inoculum in which the OTU had the highest relative abundance (INIT, blue; REG-M, gold; CO-M, red). OTUs that are closer to the points of the triangle have higher relative abundances in the microbiome type represented by that point than the other microbiome types, whereas points close to the center have similar relative abundances in all microbiome types. (d) Proportion of total sequences for each microbiome type (INIT, blue; REG-M, gold; CO-M, red) at each time point that are classified as one of the 137 OTUs that were shared across time points and across microbiome types. INIT, sterile soil reinoculated with the initial soil; REG-M, sterile soil reinoculated with bacteria cultured on regular media; CO-M, sterile soil reinoculated with bacteria cultured on media containing crude oil.