Plant growth-promoting (PGP) bacteria are an environmental-friendly alternative to chemical fertilizers for promoting plant development. We isolated and characterized a PGP endophyte, YSD J2, from the leaves of Cyperus esculentus L. var. sativus. Specific PGP characteristics of this strain, such as phosphate solubilization ability, potassium-dissolving ability, siderophore and indole-3-acetic acid (IAA) production, and salt tolerance, were determined in vitro. In addition, positive mutants were screened using the atmospheric and room-temperature plasma (ARTP) technology, with IAA level and organic phosphorus solubility as indices. Furthermore, the effect of the positive mutant on biomass production and antioxidant abilities of greengrocery seedling was evaluated and the genome was mined to explore the underlying mechanisms. The strain YSD J2 showed a good performance of PGP characteristics, such as the production of indole acetic acid and siderophores, solubilization ability of phosphate, and potassium-dissolving ability. It was recognized through 16S rRNA sequencing together with morphological and physiological tests and confirmed as Pantoea sp. The strain exposed to a mutation time of 125 s by ARTP had the highest IAA and organic phosphate (lecithin) concentrations of 10.34 mg/L and 16.52 mg/L, 42.06% and 34.15% higher than those of the initial strain. Inoculation of mutant strain YSD J2 significantly increased plant growth attributes and the activities of peroxidase and superoxide dismutase, respectively, but decreased the content of malondialdehyde significantly compared with the control. Furthermore, genome annotation and functional analysis were performed through whole-genome sequencing and PGP-related genes were identified. Our results indicated that the YSD J2 with PGP characteristics is a potential candidate for the development of biofertilizers.
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