Fig. 3: Tomato root-associated bacterial and fungal culture collections that cover the majority of species detectable by culture-independent sequencing.

a, b Phylogenetic trees showing the diversities of root-associated bacterial (a) and fungal (b) zOTUs frequently detected in the NF tomato (with a relative abundance over 0.1%). The middle ring (heatmap) represents the relative abundance of each node zOTUs presented at four different sampling locations. The outer ring (pink elliptical points) represents bacterial zOTU identified among the isolated and cultivated bacterial and fungal strains derived from NF tomato plants. LJZ, Luojiazhuang; CY, Changyi; ZY, Zhaoyuan; LD, Lindian. c Representative images of bacterial species that strongly inhibited FOL in antagonism tests. The bacterial species names, inhibition rate (%), and inhibition zone (cm) of different bacterial strain have been provided in Supplementary Data 12. In the images, the top left photograph shows the control FOL medium without inoculation of the tested bacterial strain; the middle horizontal line is the growth of the tested bacterial strain, and the growth below the line is the FOL strain. d Representative images of fungal species that strongly inhibited FOL in antagonism tests. The fungal species names are provided in Supplementary Data 13. In the images, the first top left photograph shows the control FOL medium without inoculation of the tested fungal strain; the FOL strain grows in the middle of the plate, and the tested fungal strain grows in the four corners of each plate.