Identification and Functional Analysis of Tomato MicroRNAs in the Biocontrol Bacterium Pseudomonas putida Induced Plant Resistance to Meloidogyne incognita .

Root-knot nematodes (RKNs, spp.) seriously damage tomato production worldwide, and biocontrol bacteria can induce tomato immunity to RKNs. Our previous studies have revealed that strain Sneb821 can trigger tomato immunity against . and that several long noncoding RNAs and microRNAs (miRNAs) are involved in this process. However, the molecular functions of the miRNAs in tomato immune responses remain unclear. In this study, deep small RNA sequencing identified 78 differentially expressed miRNAs in tomato plants inoculated with Sneb821 and relative to plants inoculated with alone; 38 miRNAs were upregulated, and 40 miRNAs were downregulated. The expression levels of six known miRNAs and five novel miRNAs were validated using RT-qPCR assays. These included Sly-miR482d-3p, Sly-miR156e-5p, Sly-miR319a, novel_miR_116, novel_miR_121, and novel_miR_221, which were downregulated, and Sly-miR390a-3p, Sly-miR394-3p, Sly-miR396a-3p, novel_miR_215, and novel_miR_83, which were upregulated in plants treated with Sneb821 and . In addition, Sly-miR482d was functionally characterized through gene silencing and overexpression of its target gene () in tomato and by challenging the plants with inoculation. The number of second-stage juveniles (J2) inside roots and induced galls were significantly decreased in both Sly-miR482d-silenced plants and overexpressing plants, whereas the activity of superoxide dismutase, peroxidase, and hydrogen peroxide content were significantly increased. The results suggest that Sneb821 could inhibit Sly-miR482d expression and thus regulate tomato immune responses against infestation. This study provides novel insights into the biocontrol bacteria-mediated tomato immunity to that engages with plant miRNAs.