Tomato-mediated enrichment of stress-adapted rhizobacteria under salinity and drought: a combined microbiome and cultivation-based approach

Abstract

Soil salinity and drought are major environmental constraints that increasingly threaten agricultural productivity by altering plant performance and rhizosphere microbial communities. Exploiting plant-mediated microbial recruitment under stress may represent an effective strategy for identifying potential beneficial microorganisms adapted to adverse environmental conditions. In this study, tomato plants were used as biological traps to selectively recruit and enrich stress-adapted rhizobacteria under control, salinity, and drought conditions. These bacterial communities were characterized through 16 S rRNA gene amplicon sequencing, while culturable bacteria were isolated using selective media and, subsequently, evaluated for taxonomic identity and plant growth-promoting (PGP) traits. Both salinity and drought significantly altered bacterial community composition, with treatment explaining 31% of the variation within rhizosphere communities (PERMANOVA, R² = 0.31, p = 2 × 10 − 4 ). Pairwise comparisons confirmed significant differences between control and drought (R² = 0.27, p = 0.0070), control and salinity (R² = 0.21, p = 0.0082), and salinity and drought (R² = 0.26, p = 0.0082). Among the discriminant genera identified, examples of salinity-enriched taxa were Nitrosarchaeum , Nitrosospira , Phenylobacterium , and Hydrogenophaga , while drought-enriched taxa included Massilia , Paenarthrobacter , Pseudonocardia , and Rhodoplanes . Selective cultivation yielded 127 bacterial isolates, which were grouped into 83 distinct ARDRA profiles. One representative of each profile was subjected to 16 S rRNA gene sequencing, resulting in the identification of 20 bacterial genera. The recovered collection included stress-associated genera such as Arthrobacter , Paenarthrobacter , and Streptomyces under salinity and Massilia , Microbacterium , and Lysinibacillus under drought. Several isolates displayed multiple plant growth-promoting traits, including nutrient-solubilizing activities, IAA and siderophore production, ACC deaminase activity, nitrogen fixation potential, and sulfur oxidation. Our findings demonstrate that plant-mediated recruitment under abiotic stress can be exploited as a targeted bioprospecting strategy to recover candidate stress-associated culturable bacteria with in vitro PGP traits. This approach provides a framework for identifying microbial candidates for subsequent functional validation and potential development as bioinoculants for crops exposed to salinity and drought.