In Vitro Analysis Reveals Functional Diversity, Nutrient Mobilization and Antifungal Potential of Rice Endophytic Bacteria

Endophytic bacteria play a pivotal role in plant health by modulating nutrient availability, growth regulation, and resistance to phytopathogens. However, the functional diversity and ecological significance of the endophytic bacteria in rice (Oryza sativa L.) plants remain incompletely understood. Here, we functionally characterized the diversity of endophytic bacteria isolated from healthy rice plants and evaluated their potential roles in plant growth promotion and fungal pathogen suppression under in vitro conditions. We recovered 23 bacterial isolates from roots, stems, and leaves and identified them, by means of 16S rRNA gene sequencing, as members of the genera Pseudomonas, Enterobacter, and Bacillus. Phylogenetic analysis confirmed the dominance of these genera across plant tissues. Functional characterization revealed pronounced isolate-dependent variability in the production of indole-3-acetic acid (IAA) and ammonia, and in the ability to solubilize essential macro- and micronutrients. Most isolates efficiently solubilized phosphorus (P), while potassium (K) solubilization was particularly prevalent among Bacillus isolates. In contrast, silicon (Si) and zinc (Zn) solubilization were restricted to a smaller subset of isolates, indicating functional specialization within the endophytic community. Antagonistic assays demonstrated that of the 23 isolates tested, 6 isolates inhibited the growth of Bipolaris oryzae, whereas strong suppression of Pyricularia oryzae was observed only for one Pseudomonas and one Enterobacter isolate. Limited inhibitory activity was detected against Rhizoctonia solani, which highlights pathogen-specific interactions. Altogether, our findings indicate that rice harbors functionally diverse endophytic bacteria with complementary in vitro traits related to nutrient mobilization, phytohormone production, and pathogen suppression. These results identify candidate isolates for further validation. In planta, greenhouse, and field studies are now required to establish whether these traits translate into improved plant growth, nutrient uptake, or disease control.