Fig. 4

Identification of biomarkers and key taxa to differentiate the healthy and RKN-associated root endophytic bacteria. A Top 17 bacterial orders identified to discriminate the relative abundance of endophytic microbiota in the RKN-parasitized root samples (IRH and IRK) vs healthy tomato roots, as shown by the Random Forest method. Biomarker taxa were ranked in descending order of importance for model accuracy. B Order-level biomarkers with higher relative abundance in the endophytic microbiota of healthy and parasitized tomato plants (bars = means; error bars = SE). C, D Manhattan plots showing OTUs depleted or enriched in the healthy samples vs parasitized samples IRH (C, non-gall part of root) or IRK (D, galls). Each dot or triangle represents a single OTU. OTUs enriched or depleted in the healthy tomato root are represented by filled or empty triangles, respectively (Wilcoxon rank sum test, FDR-adjusted p < 0.05). OTUs are arranged and colored according to the bacterial order. For descriptions of sample groups, see Fig. 2