Synergistic Effects of PGPR on Rhizosphere Diversity and Salinity Tolerance in Shallot (Allium cepa L. var. aggregatum)

Soil salinity, intensified by climate change, presents a major challenge to crop productivity. This study investigated the potential of plant growth-promoting bacteria (PGPB) to enhance salinity tolerance in Allium cepa L. var. aggregatum through modulation of the rhizosphere. Experimental treatments included PGPB inoculation, chemical fertilizer application, their combination, and co-inoculation of PGPB with vesicular-arbuscular mycorrhiza (VAM), each tested under control, moderate (4 dS/m), and severe (8 dS/m) salinity levels. Analyses focused on plant growth performance, Aquaporin (aqp1) gene expression, and rhizosphere metagenomics. PGPB application, especially with half-dose fertilizer under saline conditions, enhanced rhizosphere diversity and maintained Actinobacteria populations. Salinity shifted communities toward Proteobacteria, Bacteroidota, and Firmicutes while reducing Actinobacteria. The combined treatment improved phosphate availability, plant performance, and induced highest aqp1 gene expression at moderate salinity, supporting stress resilience. These findings highlight a promising, sustainable approach to improving salinity resilience in Allium cepa L. var. aggregatum cultivation while minimizing reliance on chemical fertilizers.