LAUSR

Root-knot nematodes seriously damage tomato production worldwide, and biocontrol bacteria can induce tomato immunity to RKNs. Our previous studies have revealed that Pseudomonas putida strain Sneb821 can trigger tomato immunity against M. incognita 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 M. incognita relative to plants inoculated with M. incognita 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 down-regulated, and sly-miR390a-3p, sly-miR394-3p, sly-miR396a-3p, novel_miR_215 and novel_miR_83, up-regulated in plants treated by Sneb821 and M. incognita. In addition, miR482d was functionally characterized through gene silencing and overexpression of its target gene NBS-LRR in tomato and by challenging the plants with M. incognita inoculation. The number of second-stage juveniles (J2) inside roots and induced galls were significantly decreased in both miR482d silenced plants and Solyc05g009750.1 overexpressing plants, while the activity of superoxide dismutase (SOD) and peroxidase (POD) and hydrogen peroxide (H2O2) content were significantly increased. The results suggest that Sneb821 could inhibit miR482d expression and thus regulate tomato immune responses against M. incognita infestation. This study provides novel insights into the biocontrol bacteria mediated tomato immunity to M. incognita that engages with plant miRNAs.