Fig. 2
Community composition and variation of root-associated bacteria. A Top-15 phylum-level community composition and relative abundance of root-associated bacteria at different growth stages of tomato (see “Methods” for growth stage specifications). B Unconstrained PCoA with Bray–Curtis distance showing the root-associated microbiota in healthy and RKN-parasitized samples at different growth stages of tomato plants. C Venn diagram for variance partitioning analysis (VPA) showing the variation (adjusted R2) contributed by variables “growth days,” “niche” (soil and root), and “nemato” (healthy and nematode-parasitized). Only the factors with p < 0.05 were used in the analysis. D Shannon, Chao 1 and observed species indexes of root-associated bacteria sampled in relation to growth and nematode development in tomato. HRC: healthy tomato root; HRS: healthy tomato rhizosphere soil; IRH: non-gall parts of the nematode-parasitized root; IRK: galls of the nematode-parasitized tomato root; IRS: Rhizosphere soil with RKN