| Summary: | The root microbiota contributes to the plant’s defense against stresses and pathogens. However, the co-association pattern of functional bacteria that improves plant resistance has not been interpreted clearly. Using Illumina high-throughput sequencing technology, the root bacterial community profiles of six cucumber cultivars with different resistance in response to the causative agent of cucumber <i>Fusarium</i> wilt (CFW), <i>Fusarium oxysporum</i> f. sp. <i>cucumerinum</i> (<i>Foc</i>), were analyzed. The principal coordinate analysis indicated that the interactions of the cultivars and pathogens drove the cucumber root bacterial communities (<i>p</i> = 0.001). The resistance-specific differential genera across the cultivars were identified, including <i>Massilia</i> in the resistant cultivars, unclassified Enterobacteriaceae in resistant CL11 and JY409, <i>Pseudomonas</i> in JY409, <i>Cronobacter</i> in moderately resistant ZN106, and unclassified Rhizobiaceae and <i>Streptomyces</i> in susceptible ZN6. The predominant root bacterium <i>Massilia</i> accounted for the relative abundance of up to 28.08–61.55%, but dramatically declined to 9.36% in <i>Foc</i>-inoculated susceptible ZN6. <i>Pseudomonas</i> ASV103 and ASV48 of Pseudomonadaceae and <i>Cronobacter</i> ASV162 of Enterobacteriaceae were consistently differential across the cultivars at the phylum, genus, and ASV levels. Using the culture-based method, antagonistic strains of Enterobacteriaceae with a high proportion of 51% were isolated. Furthermore, the bacterial complexes of <i>Pantoea dispersa</i> E318 + <i>Pseudomonas koreensis</i> Ps213 and <i>Cronobacter</i> spp. C1 + C7 reduced the disease index of CFW by 77.2% and 60.0% in the pot experiment, respectively. This study reveals the co-association of specific root bacteria with host plants and reveals insight into the suppressing mechanism of resistant cultivars against CFW disease by regulating the root microbiota.
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