In vitro, in planta and whole genome sequence-based elucidation of plant beneficial effects of endophytic...

This study explores the multifunctional plant beneficial traits of the endophytic bacterium Enterobacter sp. P1P isolated from the indigenous rice varieties of Kerala, India. Among the fifty seed-borne bacterial isolates screened, P1P exhibited the highest antifungal effect against the rice pathogen Rhizoctonia solani, with 55.29% fungal mycelial growth inhibition. Chemical profiling by using GC-MS has also identified several bioactive metabolites in the prepared extract of P1P, including the 2,4-di-tert-butylphenol and didemnin B which are known for their antifungal properties. In controlled pot experiments, P1P significantly enhanced the rice seedling growth, demonstrating a shoot length (20.5 ± 3.4 cm) and root length (14.3 ± 2.7 cm) which were higher when compared to the untreated control (17.9 ± 2.9 cm and 11.9 ± 1.7 cm, respectively). Moreover, P1P has also been demonstrated to have the phosphate and zinc solubilization properties along with the indole-3-acetic acid (IAA) production, the key factors contributing to plant growth promotion. Whole genome sequencing, revealed that P1P has a genome size of 4.84 Mb containing 5045 protein-coding genes, including the six biosynthetic gene clusters related to the secondary metabolites and antimicrobial peptides, such as enterobactin and saquayamycin. Genes implicated in the IAA biosynthesis (ipdc, aldH, and patA1) and mineral solubilization (gcd, gad, and pqq operon) could also be identified, highlighting its genetic basis for both the biocontrol and growth-promoting functions. By the comparative genome analysis, P1P was shown to have 99.2% average nucleotide identity with Enterobacter cloacae strains which have been previously isolated from maize. Collectively, these findings underscore the Enterobacter sp. P1P to be an eco-friendly candidate with the potential to be explored for the integrated disease management and growth enhancement for the sustainable rice cultivation.

The online version contains supplementary material available at 10.1007/s13205-026-04696-0.