Population density and functional diversity of plant growth promoting rhizobacteria associated with avocado trees in saline soils

Rhizosphere bacteria that suppress stress ethylene production via 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity play an important role in alleviation of plant stress caused by salinity and drought. While there has been considerable research on development of soil inoculants that carry this trait, relatively little is known about the population dynamics and functional diversity of indigenous ACC-degraders in field soils. Here, we surveyed plant growth promoting rhizobacteria (PGPR) that are associated with avocado trees under different degrees of stress resulting from irrigation-induced soil salinity. Variations in PGPR populations were examined for 4 rootstocks at 3 locations with levels of salinity ranging from 0.91 to 3.90 dS m−1. To characterize the culturable ACC degrading bacteria, soil water extracts from rhizosphere samples were streaked on to media containing ACC as sole nitrogen source. 105 colonies were isolated from which 20 were selected and identified by 16S rRNA gene sequence analysis. These strains were further characterized with respect to indole acetic acid (IAA) production, phosphate solubilization, and siderophore and cyanide production. Results of the survey revealed that all of the rootstocks supported indigenous ACC-degrading rhizobacteria at population densities that ranged from 1.5 × 104 to 8.5 × 106 cells g−1 rhizosphere soil, with the highest population densities occurring on the fine roots in the zone of elongation behind the root tips. The culturable ACC-degrading PGPR included species of Pseudomonas, Bacillus and Variovorax. All of the cultured isolates had different combinations of PGPR traits and varied substantially in their maximum activity levels as measured under laboratory conditions. PGPR population densities varied for the different rootstocks but were not significantly influenced by differences in soil salinity. The results suggest that indigenous PGPR are common in orchard soils, and that soil management practices that increase the population and activity of indigenous ACC degrading bacteria may serve as an alternative to soil inoculation for enhancing the stress tolerance of salt sensitive crops in saline soils.

► Indigenous plant growth promoting bacteria colonize roots of avocado trees at high cell densities.
► ACC-degrading bacteria associated with avocado trees carry multifunctional PGPR traits.
► Indigenous PGPR may confer improved tolerance of avocado to salinity and environmental stress.