Figure 2: The effect of niche conditions on the reconstructed metabolic network.

Networks were visualized following optimization in (a) bulk soil, (c) rhizosphere and (e) nodule environments. Lines are colour coded based on fitness effect of deleting each reaction: blue indicates a fitness decrease <1%; dark purple indicates a fitness decrease <50%; bright purple indicates a fitness decrease >50%; and red indicates a fitness decrease >99%. Thin grey lines indicate inactive reactions. Line thickness shows the flux through each reaction on a log scale. The graphs summarize the metabolic changes detected during the (b) bulk soil to rhizosphere and (d) rhizosphere to nodule transitions. Summary of changes graphs: on and off—reactions carrying flux only in the second and first environment, respectively; up and down—reactions carrying increased flux (≥50%) in the second and first environment, respectively; reverse—reactions whose directionality is switched; greater and lesser—reactions whose removal have a greater (≥10%) fitness impact in the second and first environment, respectively; essential and non-essential—reactions essential only in the second and first environment, respectively. The nine classifications are not mutually exclusive. The reactions present in each category are described in Supplementary Data 3 and 4. The COG analysis graphs summarize the functional annotation of the genes associated with the reactions in the summary of changes graphs. The blue and red bars include the genes associated with the blue and red bars, respectively, in the summary of changes graphs. Asterisks indicate statistically significant changes (P value <0.01) as determined by Pearson’s χ2-tests. In the reaction flux figures, each point represents the amount of flux through individual reactions in the two environments. Blue and purple symbols indicate reactions with the same or reverse directionality, respectively. The angled line indicates the position of a perfect correlation. In the reaction deletion fitness figures, each point represents the fitness of individual reaction deletion mutants in the two environments. The angled line indicates the position of a perfect correlation.