Whole-genome sequencing of Priestia megaterium EL9 provides genomic insights into multifunctional growth-promoting traits and the strain’s potential for sustainable agriculture

Long-term continuous cropping, low fertilizer use efficiency, and fixation of phosphorus and potassium in nutrient-deficient soils severely constrain sustainable tobacco production. Multifunctional plant growth-promoting rhizobacteria (PGPR) with robust environmental adaptability offer a promising strategy to reduce chemical fertilizer inputs. A multifunctional bacterial strain EL9 was isolated from tobacco rhizosphere and identified as Priestia megaterium . It showed a colorimetric value equivalent to 55.47 mg·L⁻ 1 IAA, solubilized 427.60 mg·L⁻ 1 phosphate, and mobilized 172.29 mg·L⁻ 1 potassium. Whole-genome sequencing revealed a 5.10 Mb genome carrying genetic features potentially involved in IAA production, including the tryptophan biosynthesis gene cluster and the amiE gene. Additional genes related to phosphorus transport, sulfate assimilation, and core carbon/nitrogen metabolism were also identified. Pot experiments showed that EL9 significantly increased IAA, available phosphorus, and potassium in rhizosphere soils of tobacco, Chinese cabbage, and wheat, accompanied by enhanced plant growth and root development. Field trials confirmed improved tobacco agronomic traits and cured leaf quality. Genomic safety assessment revealed no complete or obvious pathogenicity determinants based on in silico analyses, and additionally, plate assays suggested preliminary antagonistic activity against Fusarium oxysporum. Priestia megaterium EL9 is a promising multifunctional PGPR with a well-characterized genetic repertoire and showed promising efficacy in pot experiments across three crop species (tobacco, Chinese cabbage, and wheat) and in field trials with tobacco, supporting its potential as a biofertilizer for sustainable agriculture.