Endophytic drought-tolerant bacterial community dynamics across contrasting agroclimatic zones

Rice (Oryza sativa) sustains more than half of the global population but is particularly vulnerable to water limitation in rainfed upland and lowland ecosystems. Endophytic microbiomes represent a sustainable strategy for improving drought resilience, yet their diversity and functional potential in traditional rice landraces remain underexplored. This study investigated endophytic bacterial communities associated with indigenous upland and lowland cultivars of West Bengal, India, using 16S rRNA amplicon sequencing, predictive functional profiling, culture-based screening, and biochemical validation. Distinct microbial assemblages revealed for diverse agro-ecosystems, with upland cultivars enriched in stress-adapted taxa such as Proteobacteria, Actinobacteria, and Firmicutes. PICRUSt2 predictions indicated higher representation of KEGG pathways associated with osmolyte biosynthesis, antioxidant defense, and compatible solute metabolism in upland microbiomes. Culture isolates, notably Enterobacter sp. KNR1 and Klebsiella sp. GBR1, exhibited strong tolerance to PEG-induced osmotic stress, producing elevated proline, glycine betaine, EPS, and IAA, alongside efficient root colonization in susceptible rice. Collectively, these findings establish indigenous upland rice as a reservoir of functionally resilient endophytes and provide a foundation for developing microbial consortia to enhance rice performance under water-limited conditions.