Genomic prediction of phytase potential and stress tolerance in maize-associated plant growth-promoting rhizobacterium Enterobacter cloacae Mz49

Abstract

The maize rhizobacterium Enterobacter cloacae Mz49 exhibits diverse plant growth-promoting and stress-adaptive traits, indicating strong potential for bioinoculant development. Mz49 was isolated from the Egyptian rhizosphere, and demonstrated in vitro production of indole-3-acetic acid (64.89 µg/mL), antioxidant activity (IC₅₀ = 11.71 µg/mL), and anti-inflammatory properties (IC₅₀ = 63.1 µg/mL). Whole-genome sequencing revealed a 5.34 Mb genome with 5,158 protein-coding genes linked to nutrient acquisition, abiotic stress tolerance, and secondary metabolite biosynthesis. Genes associated with nitrogen fixation (nirBD, ureABCDEFGJ, amtB), phosphate solubilization (pqqIFL, phoA, pstIPN), and phytohormone synthesis (iaaT, ysnE, ipdC, ppdC, amiE) were identified. Genome analysis also revealed phytase-related genes (agp, suhB), which contribute to the release of bioavailable phosphorus, an essential nutrient for maize growth. This genetic potential highlights the strain’s contribution to enhanced plant growth and nutrient-use efficiency, particularly under phosphorus-limited conditions. Additionally, stress-response genes (sodABC, katE, betB, proABCY, dnaJK, cspA) were identified, conferring resistance to oxidative, osmotic, thermal, and cold stresses. The presence of heavy metal resistance genes (arsenic, copper, zinc, nickel) suggests suitability for use in contaminated soils. AntiSMASH analysis identified biosynthetic gene clusters for siderophores, arylpolyenes, and non-ribosomal peptides. GC–MS profiling further detected bioactive compounds, including 2, 3-butanediol, D-pinitol, succinic acid, tyrosol, and azelaic acid, which are associated with plant growth promotion and defense responses. Collectively, these findings highlight Mz49’s potential for sustainable maize cultivation, particularly in phosphorus-limited or stress-prone soils. Future research should prioritize field trials to validate its efficacy and assess potential risks associated with its application.