Fig. 3

Relative importance of the eight metabolism gene categories in predicting R. solanacearum density across plant growth in the combined datasets including healthy and diseased plants (a). Changes in relative abundance of metabolism Q genes (secondary metabolite biosynthesis, transport, and catabolism genes) in diseased and healthy plants at week 0 and week 5 (b). Relative abundance of phagotrophic protists in diseased and healthy plants at week 0 and week 5 (c). Relative abundance of Bacillus OTUs in diseased and healthy plants at week 0 and week 5 (d). Abundance of R. solanacearum in diseased and healthy plants at week 0 and week 5 (e). Co-occurrence networks between abundant phagotrophic protistan OTUs, bacterial OTUs, and metabolism Q genes for healthy and diseased plants across plant growth (f). In panel a, asterisk means P < 0.05 and three asterisks mean P < 0.001 (statistical significance was calculated by multiple regression using linear models between metabolism genes and R. solanacearum pathogen). In panel b, c, d, and e, “ns” means non-significant, asterisk means P < 0.05 and two asterisks mean P < 0.01 under student’s t test (n = 4 for metabolism Q genes, n = 8 for phagotrophic protists, Bacillus and R. solanacearum). In panel d, relative abundance of Bacillus OTUs combines the two Bacillus OTUs from the bacterial OTU table. In panel f, blue lines indicate positive, and red lines indicate negative correlations; detailed annotation of bacterial OTUs and metabolism Q genes are provided in Table S5