No, 16S rDNA gene is not the only way to identify PGPR (Plant Growth Promoting Rhizobacteria). Other molecular markers, such as 23S rDNA, gyrB, and recA genes, can also be used for the identification and characterization of PGPR. In addition to molecular techniques, biochemical and physiological tests can also be employed to identify PGPR. These tests include carbon source utilization, nitrogen fixation, phosphate solubilization, indole-3-acetic acid production, siderophore production, and ACC (1-aminocyclopropane-1-carboxylate) deaminase activity. A combination of these techniques can provide a more accurate and comprehensive identification of PGPR.
I have recently sequenced several strains of Rhizobium leguminosarum bv. trifolii, and I found 16S rDNA lacking in specificity for strain and species determination. I would recommend adding a second gene target to get better resolution.