Endophytic Bacterial Inoculants as Biostimulants: Effects on Plant Salt Tolerance and Native Rhizosphere Microbiota in Rice

Salinity is a major limiting factor for rice cultivation worldwide, with impacts worsened by climate change and water management, making salt-stress resilience an agronomic priority. A pot experiment used three rice genotypes with different salt tolerance: Oryza rufipogon (tolerant), Vialone Nano (sensitive), and introgression line IL136 (tolerant), to characterize rhizosphere microbiota changes under salt stress and inoculation with two endophytic growth-promoting strains, RCA24 (IAA producer) and RCA25 (nitrogenase activity). Four groups were compared: control, stress only, inoculation only, and stress plus inoculation, plus baseline soil. Ninety-six soil samples (16 baseline, 80 end-point) were collected and sequenced via 16S amplicon sequencing (Illumina double-PCR, AVITI platform, paired-end 300 bp). Alpha-diversity differed significantly only for species richness; Shannon and Simpson were unaffected. Beta-diversity (PCoA) showed significant separation among groups (first two axes: 36.9%, 20.8% of variance), matching heatmap clustering driven mainly by time/cultivation. LEfSe identified 12 differentially abundant taxa (LDA ≥ 2.0): 8/12 enriched in sensitive Vialone Nano, including Geobacteraceae sp., Anaeromyxobacter dehalogenans, Bacteroidales sp. and Anaerosoma tenue under stress alone, and Geobacter argillaceus, Dissulfurispira sp. and Geobacter grbiciae under stress plus inoculation. Tolerant O. rufipogon showed only two enriched taxa under stress (Rariglobus hedericola, Geomesophilobacter sediminis) and one under inoculation alone (Geothrix fermentans). IL136 showed no significantly enriched taxa. Most enriched taxa were iron-reducing/anaerobic bacteria, consistent with reduced oxygen availability in cultivated soil. These findings show that salinity and cultivation reshape rhizosphere microbiota richness and structure genotype-specifically, with the sensitive genotype showing the strongest shift toward anaerobic taxa and inoculation playing a secondary role versus genotype and stress.