Genomic features of plant growth-promoting Ochrobactrum intermedium GH3, an endophyte associated with flatsedge (Cyperus sp.) native to Hochiminh City, Vietnam.

The study investigated the plant growth-promoting (PGP) characteristics of culturable endophytic bacteria associated with a rhizomatous perennial flatsedge (Cyperus sp.) native to Hochiminh City, Vietnam. Among the six bacteria isolated, strain GH3 demonstrated the highest potency in solubilizing phosphate and producing ammonia and IAA. Genomic analysis identified strain GH3 as Ochrobactrum intermedium, showing 97.87% ANI and 86.85% alignment to GTDB reference databases. Functional annotation revealed GH3's capabilities in secondary metabolism, iron acquisition, and osmotic stress tolerance. It exhibited potential phosphate solubilization (51.33 mg/L), ammonium (2.66 mg/L), siderophore (23.50%), and IAA (12.56 mg/L) production under stress conditions. The application of strain GH3 influenced growth in rice and tomato. In rice, SL were enhanced in DT8 (27%) and ST25 (54%). Leaf emergence was stable in rice DT8 and tomato, but increased by 28.2% in rice ST25. LRN was increased in rice DT8 (34.9%) and tomato (67.2%), with no change in rice ST25. PRL extended moderately in tomato (16.9%) and rice ST25 (15.2%), but not in rice DT8, while LRL decreased in rice DT8 (-10.9%) and ST25 (-31.4%). Moreover, improvement in biomass parameters emphasized GH3's potential in biomass enhancement with species-specific effects. This study highlights the promising PGP potential of endophytic O. intermedium GH3, which could aid sustainable agriculture amid climate change. It is the first investigation into O. intermedium isolated from Cyperus species, and the first report of O. intermedium in Vietnam, offering valuable contributions to our understanding of microbial interactions within Vietnam's unique flora.